CD4ModuleID
Jack Collora
2023-06-01
Looking for modules in CD4
Looking at proliferating cells did not identify modules of significance. This further approach will be taken to identify modules across CD4s. I will be omitting those populations strongly associated with annotated CD8+ t cells identified in the annotating proliferation modules file. Those are: Central_memory, Naive_T_3, Naive_T_1, and CD8_TEMRA.
I’m also excluding proliferating, as those cells are likely to drive a proliferation module on their own that won’t be interesting given the parallel analyses.
In this case I’ll be doing similar iterations to what I did previously for the proliferating, but since there are sufficient cells, we’ll look across individuals and merge modules within treatment groups to get insteresting consensus subsets if possible.
As before, I’m checking to see there are sufficient populations to look at. In this case we do have enough to go for the most desirable, treatment + timepoint + participant split.
keep<-c("Treg", "Polarized_Effector_T", "Exhausted_Th1", "Exhausted_Memory", "Effector_Th1_CD4_and_CD8", "Th2", "CXCR5_Memory", "Naive_T_2", "Memory_T_1", "Memory_T_2")
results<-subset(results, idents = keep)## Loading required package: Signactable(results$Treatment)##
## Bup.Nalo Methadone Naltrexone
## 8193 2769 5199table(results$Timepoint)##
## 0 3
## 9701 6460table(paste(results$Treatment, results$Timepoint))##
## Bup.Nalo 0 Bup.Nalo 3 Methadone 0 Methadone 3 Naltrexone 0 Naltrexone 3
## 5302 2891 1105 1664 3294 1905table(paste(results$Treatment, results$Participant))##
## Bup.Nalo 5014 Bup.Nalo 5017 Bup.Nalo 5018 Bup.Nalo 5023 Methadone 5003
## 1530 1079 4589 995 424
## Methadone 5009 Methadone 5016 Methadone 5020 Naltrexone 5021 Naltrexone 5026
## 956 748 641 650 1866
## Naltrexone 5035 Naltrexone 5037
## 1183 1500table(paste( results$Timepoint, results$Participant))##
## 0 5003 0 5009 0 5014 0 5016 0 5017 0 5018 0 5020 0 5021 0 5023 0 5026 0 5035
## 199 160 462 327 246 3936 419 239 658 1495 556
## 0 5037 3 5003 3 5009 3 5014 3 5016 3 5017 3 5018 3 5020 3 5021 3 5023 3 5026
## 1004 225 796 1068 421 833 653 222 411 337 371
## 3 5035 3 5037
## 627 496results$P_TP<-paste(results$Participant, results$Timepoint, sep="_")
results.split<-SplitObject(results, "P_TP")
#npcs and softpowers, selecting npc based on last nonplataue pc on elbow plot, selecting softpower as first above 0.8
#repeat 1
#optional
#ran this twice, once with the standard criteria (elbow PCs + first softpower > 0.8, selecting a local maxima if 0.8 not exceeded)
#second time is replacing the softpower of the ones that dont id 3 modules at least with a softpower one lower unitl we get at least 3 (min softpower 4)
#repeated - 1, 4, 8, 11 (5021_0), 12, 15, 16, 18, 24
#commented this one out to acclerate stitching
#conds<-cbind(c(6,6,6,6,7,7,7,6,3, 6, 3, 5, 6,5,6,4, 4,4, 6, 7,5,5,6, 5) ,c(12,4,8,8,4,6,6,10,5,8,12,10,7,10,10,16, 8,16,3,8,8,3,8, 10))
#mods1<-WrapGroupModID(results.split, "NA", conds)
conds<-cbind(c(6,6,6,6,7,7,7,6,3, 6, 3, 5, 6,5,6,4, 4,4, 6, 7,5,5,6, 5 ) ,
c(5,4,8,5,4,6,6,9,5,8,7,9,7,10, 8, 7, 8,8,3,8,8,3,8, 6))
mods1<-WrapGroupModID(results.split, "NA", conds)## [1] "5018_0"
## PC_ 1
## Positive: ZEB2, AOAH, VCAN, IGKC, HDAC9, GNLY, NKG7, CCL5, PID1, ACTB
## CCSER1, TCF7L2, AUTS2, AC243829.2, TMSB10, PIP5K1B, VAV3, C1orf21, KCNQ5, ST6GALNAC3
## Negative: INPP4B, CAMK4, PAG1, SERINC5, TTC39C, CASK, CDC14A, HIVEP2, RORA, ARHGAP15
## ANK3, TNIK, TNFAIP8, MDFIC, LEF1, SKAP1, DOCK10, ITGB1, KLF12, RASGRF2
## PC_ 2
## Positive: LINC02694, IKZF2, AC013652.1, TTN, AC093865.1, CDHR3, RTKN2, STAM, CCDC141, TOX
## DUSP4, CTLA4, IL2RA, HPGD, ST8SIA6, F5, FANK1, TSHR, MCF2L2, ADAM12
## Negative: ANK3, NELL2, RASGRF2, NR3C2, THEMIS, IFNG-AS1, ITGA4, SBF2, AC139720.1, DPP4
## PLCB1, BCL2, BTBD11, MYBL1, TAFA1, INPP4B, UST, RBMS1, SATB1-AS1, PRKN
## PC_ 3
## Positive: TGFBR3, C1orf21, AOAH, PPP2R2B, PDGFD, AC243829.2, ZEB2, AGAP1, NCALD, DTHD1
## SYTL2, PARP8, THEMIS, GTDC1, MYBL1, PZP, A2M, LINC02384, SLC4A4, HIVEP3
## Negative: LEF1, TSHZ2, PRKCA, FHIT, TXK, SESN3, PLCL1, FAAH2, CMTM8, MAP3K1
## SERINC5, KANK1, AL589693.1, AC139720.1, PVT1, LTB, AC233976.1, FAM13A, TIAM1, BCL2
## PC_ 4
## Positive: GCNT4, AL353660.1, ST8SIA1, TOX, LINC01934, RBMS3, SGPP2, IKZF2, LEF1, AC093865.1
## TAFA2, SESN3, ITGA4, TXK, SLC14A1, C12orf42, BICDL1, MALAT1, GLCCI1, MAML2
## Negative: FRY, ADAM12, PTPN13, PLD1, AL589693.1, ADAM19, LINC00299, RUNX2, CCR6, MCF2L2
## COL5A3, B4GALT5, PLCB1, ANTXR2, MB21D2, HLF, ANKRD28, EEPD1, ZNF462, CEP112
## PC_ 5
## Positive: VCAN, ZEB2, PID1, HDAC9, VAV3, TCF7L2, BACH1, PDE4D, MAML3, CCSER1
## PCSK5, AOAH, IGF1R, SBF2, JAZF1, PELI2, NRIP1, MAP3K1, S100Z, AUTS2
## Negative: ERN1, SLF1, ST8SIA1, LRIG1, GNAO1, ANK3, THEMIS, RORA, KIAA0825, PCAT1
## ITGB1, PLEKHA5, ADAM19, BICDL1, INPP4B, IL18R1, DLGAP1, LINC01934, SERINC5, SMC4
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 3.70e-01 14.9000 0.894 1.07e+02 1.07e+02 1.13e+02
## 2 2 8.56e-02 2.6200 0.907 5.52e+01 5.51e+01 6.21e+01
## 3 3 4.07e-05 -0.0367 0.820 2.86e+01 2.84e+01 3.45e+01
## 4 4 7.46e-02 -1.1800 0.877 1.49e+01 1.47e+01 1.94e+01
## 5 5 2.11e-01 -1.6500 0.794 7.79e+00 7.60e+00 1.10e+01
## 6 6 3.60e-01 -1.8400 0.731 4.10e+00 3.94e+00 6.34e+00
## 7 7 5.90e-01 -2.3600 0.748 2.17e+00 2.05e+00 3.70e+00
## 8 8 5.40e-01 -2.5000 0.588 1.16e+00 1.07e+00 2.18e+00
## 9 9 6.84e-01 -2.2700 0.765 6.22e-01 5.65e-01 1.30e+00
## 10 10 7.50e-01 -2.5000 0.766 3.36e-01 2.98e-01 7.81e-01
## 11 12 8.87e-01 -2.3000 0.881 1.00e-01 8.55e-02 2.89e-01
## 12 14 9.62e-01 -2.1000 0.954 3.10e-02 2.43e-02 1.10e-01
## 13 16 9.54e-01 -1.9400 0.942 9.90e-03 7.04e-03 4.30e-02
## 14 18 9.43e-01 -1.7100 0.933 3.29e-03 2.08e-03 1.71e-02
## 15 20 2.90e-01 -3.4500 0.171 1.15e-03 6.46e-04 9.17e-03
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6
## 107 29 26 16 11 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 7 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $yellow
## [1] "INPP4B" "CAMK4" "PAG1" "SERINC5" "TTC39C"
## [6] "CASK" "CDC14A" "HIVEP2" "RORA" "ARHGAP15"
## [11] "ANK3" "TNIK" "TNFAIP8" "MDFIC" "LEF1"
## [16] "SKAP1" "DOCK10" "ITGB1" "KLF12" "RASGRF2"
## [21] "SORL1" "PVT1" "RUNX1" "FAAH2" "PCAT1"
## [26] "NELL2" "NR3C2" "THEMIS" "ITGA4" "AC139720.1"
## [31] "DPP4" "BCL2" "BTBD11" "TAFA1" "UST"
## [36] "RBMS1" "SATB1-AS1" "PRKN" "MAN1C1" "LINC01934"
## [41] "FMN1" "FKBP5" "RNF157" "PARP8" "TSHZ2"
## [46] "PRKCA" "TXK" "SESN3" "PLCL1" "CMTM8"
## [51] "MAP3K1" "KANK1" "AC233976.1" "AL353660.1" "RETREG1"
## [56] "ST8SIA1" "MALAT1" "MAML2" "MLLT3" "SPON1"
## [61] "ADAM19" "MB21D2" "GREM2" "ERN1" "LRIG1"
## [66] "SAMD12"
##
## $brown
## [1] "LINC02694" "IKZF2" "AC013652.1" "TTN" "AC093865.1"
## [6] "CDHR3" "RTKN2" "STAM" "CCDC141" "TOX"
## [11] "DUSP4" "CTLA4" "IL2RA" "HPGD" "ST8SIA6"
## [16] "F5" "FANK1" "TSHR" "ATXN7L1" "TAFA2"
## [21] "MIR181A1HG" "SLC16A10" "GCNT4" "RBMS3" "SGPP2"
## [26] "SLC14A1" "GLCCI1"
##
## $red
## [1] "MCF2L2" "ADAM12" "AL136456.1" "AL589693.1" "FRY"
## [6] "PTPN13" "RUNX2" "CCR6" "ANK1" "DUSP16"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "11/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "INPP4B" "CAMK4" "PAG1" "SERINC5" "TTC39C"
## [6] "CASK" "CDC14A" "HIVEP2" "RORA" "ARHGAP15"
## [11] "ANK3" "TNIK" "TNFAIP8" "MDFIC" "LEF1"
## [16] "SKAP1" "DOCK10" "ITGB1" "KLF12" "RASGRF2"
## [21] "SORL1" "PVT1" "RUNX1" "FAAH2" "PCAT1"
## [26] "NELL2" "NR3C2" "THEMIS" "ITGA4" "AC139720.1"
## [31] "DPP4" "BCL2" "BTBD11" "TAFA1" "UST"
## [36] "RBMS1" "SATB1-AS1" "PRKN" "MAN1C1" "LINC01934"
## [41] "FMN1" "FKBP5" "RNF157" "PARP8" "TSHZ2"
## [46] "PRKCA" "TXK" "SESN3" "PLCL1" "CMTM8"
## [51] "MAP3K1" "KANK1" "AC233976.1" "AL353660.1" "RETREG1"
## [56] "ST8SIA1" "MALAT1" "MAML2" "MLLT3" "SPON1"
## [61] "ADAM19" "MB21D2" "GREM2" "ERN1" "LRIG1"
## [66] "SAMD12"
##
## $brown
## [1] "LINC02694" "IKZF2" "AC013652.1" "TTN" "AC093865.1"
## [6] "CDHR3" "RTKN2" "STAM" "CCDC141" "TOX"
## [11] "DUSP4" "CTLA4" "IL2RA" "HPGD" "ST8SIA6"
## [16] "F5" "FANK1" "TSHR" "ATXN7L1" "TAFA2"
## [21] "MIR181A1HG" "SLC16A10" "GCNT4" "RBMS3" "SGPP2"
## [26] "SLC14A1" "GLCCI1"
##
## $red
## [1] "MCF2L2" "ADAM12" "AL136456.1" "AL589693.1" "FRY"
## [6] "PTPN13" "RUNX2" "CCR6" "ANK1" "DUSP16"
##
## [1] "5018_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8401## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50231## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 5.332e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: AC105402.3, RPL41, RPL19, RPS18, RPS19, RPL37A, AOAH, BANK1, NKG7, AC243829.2
## CDH4, SPON2, RPL28, GNLY, RPL18A, PRSS23, WDFY4, AL450352.1, C1orf21, RPS28
## Negative: ARHGAP15, PAG1, DPYD, MBNL1, RORA, CNOT6L, LINC01619, KLF12, ANTXR2, GNAQ
## PPP3CA, GPRIN3, PARP8, ZBTB20, RBMS1, CDC14A, SKAP1, GLS, FBXL17, TMEM65
## PC_ 2
## Positive: ANK3, MYBL1, THEMIS, RASGRF2, INPP4B, PLCB1, ITGA4, BTBD11, PARP8, BACH2
## DPP4, NR3C2, SBF2, RBMS1, PIK3R1, ATP10A, PZP, AOAH, LINC01934, SCML4
## Negative: TTN, IKZF2, LINC02694, CCDC141, AC093865.1, STAM, CDHR3, AC013652.1, MIR181A1HG, TAFA2
## CENPF, AL136456.1, PALM2-AKAP2, ATXN7L1, F5, RTKN2, ABLIM1, MKI67, TOX, DTL
## PC_ 3
## Positive: ZEB2, AOAH, C1orf21, GNLY, PDGFD, ARHGAP26, ADGRG5, RRM2, AC243829.2, RAD51
## CBLB, MCTP2, STMN1, SAMD3, DTHD1, NCAPG, LYN, IL18RAP, PPP2R2B, PLCB1
## Negative: TSHZ2, PRKCA, AL589693.1, LEF1, KANK1, CMTM8, PLCL1, FMN1, TIAM1, PAG1
## PTPN13, FAAH2, MCF2L2, INPP4B, CDC14A, FRY, AC233976.1, LDLRAD4, SESN3, SAMD12
## PC_ 4
## Positive: LINC02694, CCDC141, AC013652.1, CDHR3, ARHGAP26, IKZF2, HPGD, MIR4435-2HG, ZEB2, C1orf21
## AOAH, TTN, AC093865.1, ARL15, TOX, MSC-AS1, STAM, PPP2R2B, DCP1B, NIBAN1
## Negative: TOP2A, KIF4A, DIAPH3, STMN1, RAD51, CIT, SGO2, DTL, DLGAP5, RRM2
## POLQ, CKAP2L, ESPL1, HJURP, CEP55, AURKA, STIL, HIST1H3B, KIF14, NCAPG
## PC_ 5
## Positive: RPL28, RPL41, RPS28, RPS19, RPS18, TMSB10, EEF1A1, RPL18A, LTB, RPL37A
## RPL37, RPL19, IL32, A2M, CR1, AC013652.1, FRY, PLCG2, PZP, GRN
## Negative: ST8SIA1, ITGA4, GCNT4, TRPS1, CHN1, PHEX, KIAA1671, AHCYL2, LEF1, UBASH3B
## CYP7B1, FHIT, APBA2, VPS54, SGPP2, LINC00598, BCAS3, AL353660.1, BICDL1, L3MBTL4
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.0407 -7.60 0.646 113.0000 1.13e+02 119.00
## 2 2 0.3270 -10.30 0.698 58.5000 5.79e+01 66.50
## 3 3 0.5740 -8.53 0.680 30.6000 3.00e+01 39.00
## 4 4 0.7030 -6.90 0.718 16.2000 1.57e+01 24.20
## 5 5 0.3230 -12.40 0.161 8.6900 8.36e+00 16.10
## 6 6 0.3330 -12.20 0.142 4.7400 4.47e+00 11.40
## 7 7 0.3640 -7.46 0.201 2.6500 2.41e+00 8.55
## 8 8 0.3830 -9.35 0.210 1.5100 1.31e+00 6.74
## 9 9 0.3870 -6.72 0.237 0.8900 7.33e-01 5.53
## 10 10 0.3250 -6.16 0.133 0.5420 4.06e-01 4.67
## 11 12 0.3900 -5.25 0.250 0.2260 1.28e-01 3.54
## 12 14 0.3830 -4.84 0.212 0.1110 4.17e-02 2.84
## 13 16 0.3000 -3.81 0.102 0.0646 1.41e-02 2.37
## 14 18 0.3660 -3.68 0.209 0.0427 4.81e-03 2.04
## 15 20 0.3860 -3.41 0.224 0.0312 1.70e-03 1.80
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8
## 13 46 38 37 30 18 15 15 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.## $turquoise
## [1] "AC105402.3" "BANK1" "WDFY4" "UBE2E2" "RALGPS2"
## [6] "MBNL1" "RORA" "LINC01619" "KLF12" "PPP3CA"
## [11] "GPRIN3" "ZBTB20" "GLS" "FBXL17" "THEMIS"
## [16] "RASGRF2" "BTBD11" "BACH2" "DPP4" "NR3C2"
## [21] "SBF2" "LYN" "CR1" "GRN" "CRIP2"
## [26] "KAT2B" "LINC00299" "B4GALT5" "SNX9" "MB21D2"
## [31] "TANC2" "RNF157" "BLK" "CDK14" "EBF1"
## [36] "USP6NL" "MEF2C" "MARCH1" "HLA-DQA1" "COBLL1"
## [41] "PLXDC2" "TBC1D9" "PAXBP1-AS1" "FAM49A" "MTSS1"
## [46] "LINC00665"
##
## $pink
## [1] "RPL41" "RPL19" "RPS19" "RPL37A" "RPL18A" "RPS28" "RPL37" "TMSB10"
## [9] "LTB" "IL32"
##
## $brown
## [1] "RPS18" "RPL28" "AL450352.1" "PLCG2" "CENPF"
## [6] "MKI67" "DTL" "STIL" "RRM2" "RAD51"
## [11] "STMN1" "NCAPG" "KIF15" "CIT" "TOP2A"
## [16] "KIF4A" "DIAPH3" "SGO2" "DLGAP5" "POLQ"
## [21] "CKAP2L" "ESPL1" "HJURP" "CEP55" "AURKA"
## [26] "HIST1H3B" "KIF14" "ANLN" "CDCA2" "KIF18A"
## [31] "DEPDC1B" "SHCBP1" "EEF1A1" "LMNA" "FILIP1L"
## [36] "GATA3" "ZBTB16"
##
## $red
## [1] "AOAH" "NKG7" "AC243829.2" "GNLY" "PRSS23"
## [6] "C1orf21" "EPB41L4A" "PZP" "A2M" "ZEB2"
## [11] "PDGFD" "ADGRG5" "DTHD1" "KLRK1" "CCL5"
##
## $black
## [1] "SPON2" "TMCC3" "MYBL1" "PLCB1" "ATP10A" "IFNG-AS1"
## [7] "FNDC3B" "PELI2" "ARHGAP26" "MCTP2" "SAMD3" "IL18RAP"
## [13] "PPP2R2B" "L3MBTL4" "SYTL2"
##
## $blue
## [1] "ARHGAP15" "PAG1" "RBMS1" "CDC14A" "TMEM65"
## [6] "AKT3" "INPP4B" "ANK3" "UST" "PRKCA"
## [11] "AL589693.1" "LEF1" "KANK1" "CMTM8" "FMN1"
## [16] "TIAM1" "PTPN13" "FAAH2" "FRY" "AC233976.1"
## [21] "SESN3" "SAMD12" "AC139720.1" "FHIT" "RETREG1"
## [26] "BCL2" "ST8SIA1" "GCNT4" "CHN1" "PHEX"
## [31] "VPS54" "AL353660.1" "BICDL1" "FAM160A1" "ADAM19"
## [36] "CCR6" "AFF3" "FCHSD2"
##
## $green
## [1] "DPYD" "ANTXR2" "GNAQ" "SKAP1" "PAM"
## [6] "TTN" "IKZF2" "LINC02694" "CCDC141" "AC093865.1"
## [11] "STAM" "CDHR3" "AC013652.1" "MIR181A1HG" "TAFA2"
## [16] "AL136456.1" "PALM2-AKAP2" "ATXN7L1" "F5" "RTKN2"
## [21] "ABLIM1" "TOX" "ENTPD1" "LDLRAD4" "TSHR"
## [26] "ADAM12" "TSHZ2" "PLCL1" "MCF2L2" "ITGB1"
## [31] "HPGD" "MIR4435-2HG" "ARL15" "MSC-AS1" "DCP1B"
## [36] "NIBAN1" "JAZF1" "ST8SIA6" "KIAA1671" "AHCYL2"
## [41] "UBASH3B" "CYP7B1" "SGPP2" "BCAS3" "SH3RF3"
## [46] "CD247" "RBMS3" "PLD1"
##
## [1] "8840/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "155/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $pink
## [1] "RPL41" "RPL19" "RPS19" "RPL37A" "RPL18A" "RPS28" "RPL37" "TMSB10"
## [9] "LTB" "IL32"
##
## $brown
## [1] "RPS18" "RPL28" "AL450352.1" "PLCG2" "CENPF"
## [6] "MKI67" "DTL" "STIL" "RRM2" "RAD51"
## [11] "STMN1" "NCAPG" "KIF15" "CIT" "TOP2A"
## [16] "KIF4A" "DIAPH3" "SGO2" "DLGAP5" "POLQ"
## [21] "CKAP2L" "ESPL1" "HJURP" "CEP55" "AURKA"
## [26] "HIST1H3B" "KIF14" "ANLN" "CDCA2" "KIF18A"
## [31] "DEPDC1B" "SHCBP1" "EEF1A1" "LMNA" "FILIP1L"
## [36] "GATA3" "ZBTB16"
##
## $red
## [1] "AOAH" "NKG7" "AC243829.2" "GNLY" "PRSS23"
## [6] "C1orf21" "EPB41L4A" "PZP" "A2M" "ZEB2"
## [11] "PDGFD" "ADGRG5" "DTHD1" "KLRK1" "CCL5"
##
## $black
## [1] "SPON2" "TMCC3" "MYBL1" "PLCB1" "ATP10A" "IFNG-AS1"
## [7] "FNDC3B" "PELI2" "ARHGAP26" "MCTP2" "SAMD3" "IL18RAP"
## [13] "PPP2R2B" "L3MBTL4" "SYTL2"
##
## $blue
## [1] "ARHGAP15" "PAG1" "RBMS1" "CDC14A" "TMEM65"
## [6] "AKT3" "INPP4B" "ANK3" "UST" "PRKCA"
## [11] "AL589693.1" "LEF1" "KANK1" "CMTM8" "FMN1"
## [16] "TIAM1" "PTPN13" "FAAH2" "FRY" "AC233976.1"
## [21] "SESN3" "SAMD12" "AC139720.1" "FHIT" "RETREG1"
## [26] "BCL2" "ST8SIA1" "GCNT4" "CHN1" "PHEX"
## [31] "VPS54" "AL353660.1" "BICDL1" "FAM160A1" "ADAM19"
## [36] "CCR6" "AFF3" "FCHSD2"
##
## $green
## [1] "DPYD" "ANTXR2" "GNAQ" "SKAP1" "PAM"
## [6] "TTN" "IKZF2" "LINC02694" "CCDC141" "AC093865.1"
## [11] "STAM" "CDHR3" "AC013652.1" "MIR181A1HG" "TAFA2"
## [16] "AL136456.1" "PALM2-AKAP2" "ATXN7L1" "F5" "RTKN2"
## [21] "ABLIM1" "TOX" "ENTPD1" "LDLRAD4" "TSHR"
## [26] "ADAM12" "TSHZ2" "PLCL1" "MCF2L2" "ITGB1"
## [31] "HPGD" "MIR4435-2HG" "ARL15" "MSC-AS1" "DCP1B"
## [36] "NIBAN1" "JAZF1" "ST8SIA6" "KIAA1671" "AHCYL2"
## [41] "UBASH3B" "CYP7B1" "SGPP2" "BCAS3" "SH3RF3"
## [46] "CD247" "RBMS3" "PLD1"
##
## [1] "5014_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.689## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50151## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.7471e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: RPLP2, RPL41, RPS19, IGKC, IL32, ARHGAP24, MALAT1, FOS, AC022217.3, JUN
## HDAC9, CD74, BANK1, FOSB, CD79A, MEF2C, WDFY4, IGHM, COL19A1, MS4A1
## Negative: ARHGAP15, SOS1, RORA, DPYD, RPS6KA3, PARP8, KAT2B, MBNL1, STAT4, PAG1
## CNOT6L, ATXN1, CDC14A, JMJD1C, THEMIS, RBMS1, BBS9, OSBPL3, TC2N, RABGAP1L
## PC_ 2
## Positive: PRKCA, LEF1, SERINC5, TSHZ2, SESN3, PLCL1, MAML2, CMTM8, AL353660.1, MAP3K1
## AC139720.1, INPP4B, UBASH3B, CSGALNACT1, AC233976.1, MALAT1, GCNT4, FAAH2, RETREG1, TIAM1
## Negative: PLCB1, ZEB2, ARHGAP26, C1orf21, LINC00299, TGFBR3, SYTL2, GNLY, NCALD, AGAP1
## IL18RAP, PPP2R2B, LINC02384, AUTS2, MYBL1, SETBP1, AOAH, TMCC3, STAT4, GTDC1
## PC_ 3
## Positive: PLXDC2, UGGT2, MEF2C, LRMDA, BACE2, LYN, DAPK1, DACH1, KHDRBS2, ADAM28
## AFF3, USP6NL, ARHGAP24, BANK1, CDK14, MYB, PDE3A, MED12L, MCTP1, CTDSPL
## Negative: ANK3, TC2N, RORA, MYBL1, THEMIS, STAT4, PARP8, RASGRF2, IL18RAP, IFNG-AS1
## EML4, PLCB1, TPRG1, SYTL2, PDE3B, DPP4, IL18R1, CD96, A2M, TGFBR3
## PC_ 4
## Positive: ANK3, NELL2, BACH2, PCSK5, RASGRF2, PRKN, NR3C2, AC139720.1, INPP4B, FMN1
## ADAM23, RPLP2, MAN1C1, USP6NL, ZNF516, IGF1R, ZBTB20, IFNG-AS1, THEMIS, ARHGAP32
## Negative: IKZF2, AC093865.1, LINC02694, TOX, F5, AC013652.1, RTKN2, ST8SIA6, TTN, IL2RA
## STAM, CCDC141, PSD3, VAV3, NUSAP1, AL136456.1, MCF2L2, BRCA2, RBMS3, NIBAN1
## PC_ 5
## Positive: BANK1, MS4A1, OSBPL10, TBC1D9, TCF4, ARHGAP24, MEF2C, KHDRBS2, IGKC, AFF3
## MARCH1, RALGPS2, CCSER1, WDFY4, COL19A1, CD74, PLEKHG1, IGHM, UBE2E2, FCRL5
## Negative: LSM2, AC078778.1, NKAIN2, SLC35G2, CACNB2, CDC42BPA, PBX1, ETS2, GOLIM4, AC055811.1
## MINPP1, RNF217, SLC40A1, AC010745.2, MEIS1, MYB, ITGA9-AS1, DPY19L2, PRKG2, ARHGEF28
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.0378 7.25 0.8760 1.16e+02 1.15e+02 122.000
## 2 2 0.0212 2.52 0.7840 5.97e+01 5.93e+01 66.400
## 3 3 0.0109 -1.09 0.8360 3.12e+01 3.09e+01 37.100
## 4 4 0.1470 -2.86 0.8610 1.65e+01 1.62e+01 21.400
## 5 5 0.3050 -3.36 0.8270 8.84e+00 8.57e+00 12.700
## 6 6 0.5300 -3.75 0.8470 4.81e+00 4.59e+00 7.770
## 7 7 0.6850 -3.66 0.8290 2.66e+00 2.50e+00 4.910
## 8 8 0.8390 -3.28 0.8780 1.50e+00 1.37e+00 3.190
## 9 9 0.2820 -7.17 0.1360 8.61e-01 7.61e-01 2.130
## 10 10 0.8910 -2.72 0.8630 5.05e-01 4.31e-01 1.470
## 11 12 0.9410 -2.32 0.9250 1.86e-01 1.40e-01 0.797
## 12 14 0.9390 -1.99 0.9240 7.57e-02 4.64e-02 0.461
## 13 16 0.1580 -2.48 -0.0318 3.37e-02 1.64e-02 0.280
## 14 18 0.1660 -2.27 -0.0301 1.64e-02 6.13e-03 0.175
## 15 20 0.2090 -2.29 -0.0131 8.57e-03 2.35e-03 0.118
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 165 27 13 12 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $brown
## [1] "IGKC" "ARHGAP24" "CD74" "BANK1" "CD79A" "MEF2C"
## [7] "IGHM" "COL19A1" "MS4A1" "PLXDC2" "AFF3" "SWAP70"
##
## $yellow
## [1] "RORA" "PARP8" "STAT4" "THEMIS" "PLCB1" "LINC00299"
## [7] "SYTL2" "IL18RAP" "MYBL1" "MVB12B"
##
## $turquoise
## [1] "LRMDA" "DACH1" "MYB" "PDE3A" "CTDSPL"
## [6] "SLC40A1" "AC078778.1" "ICA1" "LSM2" "SLC35G2"
## [11] "CACNB2" "CDC42BPA" "PBX1" "ETS2" "GOLIM4"
## [16] "AC055811.1" "MINPP1" "RNF217" "AC010745.2" "MEIS1"
## [21] "ITGA9-AS1" "DPY19L2" "ARHGEF28" "MERTK" "MGST2"
## [26] "DEPTOR" "AF233439.1"
##
## $blue
## [1] "ST5" "KIF11" "CIT" "CENPM" "CDCA8"
## [6] "KNL1" "ESCO2" "CDC25A" "HIST1H2AL" "FOXM1"
## [11] "DTL" "BX004807.1" "SOX2-OT"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "IGKC" "ARHGAP24" "CD74" "BANK1" "CD79A" "MEF2C"
## [7] "IGHM" "COL19A1" "MS4A1" "PLXDC2" "AFF3" "SWAP70"
##
## $yellow
## [1] "RORA" "PARP8" "STAT4" "THEMIS" "PLCB1" "LINC00299"
## [7] "SYTL2" "IL18RAP" "MYBL1" "MVB12B"
##
## $turquoise
## [1] "LRMDA" "DACH1" "MYB" "PDE3A" "CTDSPL"
## [6] "SLC40A1" "AC078778.1" "ICA1" "LSM2" "SLC35G2"
## [11] "CACNB2" "CDC42BPA" "PBX1" "ETS2" "GOLIM4"
## [16] "AC055811.1" "MINPP1" "RNF217" "AC010745.2" "MEIS1"
## [21] "ITGA9-AS1" "DPY19L2" "ARHGEF28" "MERTK" "MGST2"
## [26] "DEPTOR" "AF233439.1"
##
## $blue
## [1] "ST5" "KIF11" "CIT" "CENPM" "CDCA8"
## [6] "KNL1" "ESCO2" "CDC25A" "HIST1H2AL" "FOXM1"
## [11] "DTL" "BX004807.1" "SOX2-OT"
##
## [1] "5023_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8432## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50212## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.747e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, CDC14A, INPP4B, ANK3, MDFIC, THEMIS, MBNL1, RORA, DOCK10, PRKCA
## GPRIN3, SOS1, PARP8, PDE3B, LEF1, RBMS1, KLF12, RUNX2, DPYD, SKAP1
## Negative: RPL41, BANK1, RPL13A, RPS23, RPLP1, RPL28, RPS18, LYN, RPL13, RPLP2
## ZEB2, AFF3, RPS2, RPL3, EBF1, TMSB10, RPS19, VCAN, RPL12, RPL18A
## PC_ 2
## Positive: ZEB2, AOAH, LYN, C1orf21, GTDC1, ARHGAP26, BANK1, SETBP1, DTHD1, PDGFD
## TGFBR3, MAP3K8, GAS7, VCAN, KLRK1, SAMD3, LINC02384, PPP2R2B, EBF1, NCALD
## Negative: PRKCA, LEF1, INPP4B, LTB, AC139720.1, TSHZ2, RPL13, TMSB10, RPL13A, CMTM8
## RPS18, RPS28, RPLP2, EEF1A1, RPL18, ANK3, RPL3, KANK1, TXK, FHIT
## PC_ 3
## Positive: RPLP2, RPS19, RPS2, RPS28, RPL28, RPL18A, RPL13, EEF1A1, RPS23, LTB
## RPLP1, RPL12, RPL18, RPL3, RPS18, RPL41, AP001011.1, TMSB10, RPL13A, TRBC2
## Negative: ZSWIM5, PLCB1, PRKCA, BTBD11, MYO1D, SDK2, EFCAB8, TIAM1, IGF1R, ELOVL6
## CNNM2, PLXNA4, MAP2K6, SAMD12, EXPH5, TTLL11, EPHB1, ACYP2, ZFYVE9, TAFA1
## PC_ 4
## Positive: LINC02694, TOX, TSHR, CDHR3, SLC9A9, TTN, IKZF2, CCDC141, AC013652.1, AC093865.1
## RTKN2, STAM, F5, IL7, ATXN7L1, CYTOR, TSHZ2, ZC2HC1A, LINC01362, FHIT
## Negative: PDE4D, PLCB1, BACH2, ADAM23, NELL2, RBMS1, MYBL1, SBF2, PZP, NRIP1
## PCSK5, EDA, A2M, NR3C2, UBE2E2, RPS2, CR1, ALOX5, SNTG2, CFH
## PC_ 5
## Positive: BANK1, LYN, CERS6, EBF1, VCAN, DMXL2, AFF3, GRK3, CCSER1, PLXDC2
## IGKC, ZEB2, TRIO, MTSS1, APBA2, IGF1R, MAML3, NEXMIF, SETBP1, SESN3
## Negative: LINC00299, FRY, PLCB1, MSC-AS1, RORA, B4GALT5, AL136456.1, NTN4, LINC02694, SYTL2
## NCALD, MYBL1, RUNX2, IL18RAP, IL18R1, PTPN13, TRIQK, CASC8, PDE4D, DLEU1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.666 -29.20 0.804 1.03e+02 1.03e+02 109.0000
## 2 2 0.572 -14.70 0.654 5.32e+01 5.28e+01 59.9000
## 3 3 0.512 -7.94 0.716 2.77e+01 2.73e+01 33.3000
## 4 4 0.514 -5.66 0.818 1.46e+01 1.42e+01 18.8000
## 5 5 0.489 -3.93 0.712 7.79e+00 7.49e+00 10.8000
## 6 6 0.489 -2.53 0.580 4.21e+00 3.96e+00 6.2900
## 7 7 0.499 -2.06 0.437 2.31e+00 2.13e+00 3.8600
## 8 8 0.867 -2.50 0.832 1.29e+00 1.16e+00 2.6000
## 9 9 0.902 -2.40 0.875 7.33e-01 6.23e-01 1.8000
## 10 10 0.956 -2.23 0.962 4.26e-01 3.42e-01 1.2800
## 11 12 0.894 -1.84 0.944 1.54e-01 1.04e-01 0.6850
## 12 14 0.786 -1.61 0.781 6.07e-02 3.25e-02 0.3800
## 13 16 0.878 -1.40 0.908 2.62e-02 1.05e-02 0.2160
## 14 18 0.811 -1.29 0.807 1.22e-02 3.41e-03 0.1240
## 15 20 0.896 -1.19 0.890 5.98e-03 1.17e-03 0.0717
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8
## 68 37 20 17 16 13 12 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.## $turquoise
## [1] "ARHGAP15" "CDC14A" "INPP4B" "ANK3" "MDFIC"
## [6] "THEMIS" "MBNL1" "DOCK10" "PRKCA" "GPRIN3"
## [11] "PARP8" "PDE3B" "LEF1" "KLF12" "DPYD"
## [16] "EPHA4" "SUPT3H" "MAML2" "GNAQ" "LPP"
## [21] "AC139720.1" "TSHZ2" "CMTM8" "TXK" "FHIT"
## [26] "FAAH2" "ACYP2" "TAFA1" "SLC9A9" "LINC01362"
## [31] "LINC01727" "ST8SIA1" "NELL2" "NR3C2" "RASGRF2"
## [36] "PCAT1" "PLCL1"
##
## $blue
## [1] "RORA" "SOS1" "RBMS1" "RUNX2" "PLCB1" "ZSWIM5"
## [7] "ELOVL6" "CNNM2" "PDE4D" "MYBL1" "CR1" "SNTG2"
## [13] "ABCB1" "LINC00299" "FRY" "B4GALT5" "TRIQK" "TNFAIP3"
## [19] "DST" "MTUS2"
##
## $black
## [1] "BANK1" "LYN" "ZEB2" "AFF3" "EBF1" "VCAN" "IGKC" "SETBP1"
## [9] "AOAH" "MAP3K8" "GRK3" "PLXDC2" "SKAP2" "UBE2E2" "ALOX5" "DMXL2"
## [17] "CCSER1" "TRIO" "MAML3" "TCF7L2"
##
## $yellow
## [1] "RPS23" "RPLP1" "RPL28" "RPS18" "RPL13" "RPLP2" "RPS2" "RPL3"
## [9] "TMSB10" "RPS19" "RPS28" "EEF1A1" "RPL18" "TRBC1" "TRBC2" "ID2"
##
## $green
## [1] "C1orf21" "GTDC1" "DTHD1" "PDGFD" "TGFBR3" "GAS7"
## [7] "KLRK1" "SAMD3" "LINC02384" "PPP2R2B" "NCALD" "SYTL2"
## [13] "MCTP2"
##
## $brown
## [1] "AC013652.1" "LINC02694" "TOX" "TSHR" "CDHR3"
## [6] "TTN" "IKZF2" "CCDC141" "AC093865.1" "RTKN2"
## [11] "STAM" "IL7" "ATXN7L1" "CYTOR" "ZC2HC1A"
## [16] "XYLB" "EZH2"
##
## $red
## [1] "F5" "AL136456.1" "NTN4" "PTPN13" "DLEU1"
## [6] "CYTH3" "AL589693.1" "COL5A3" "NEDD4L" "MCF2L2"
## [11] "MAPK10" "KLF7"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "ARHGAP15" "CDC14A" "INPP4B" "ANK3" "MDFIC"
## [6] "THEMIS" "MBNL1" "DOCK10" "PRKCA" "GPRIN3"
## [11] "PARP8" "PDE3B" "LEF1" "KLF12" "DPYD"
## [16] "EPHA4" "SUPT3H" "MAML2" "GNAQ" "LPP"
## [21] "AC139720.1" "TSHZ2" "CMTM8" "TXK" "FHIT"
## [26] "FAAH2" "ACYP2" "TAFA1" "SLC9A9" "LINC01362"
## [31] "LINC01727" "ST8SIA1" "NELL2" "NR3C2" "RASGRF2"
## [36] "PCAT1" "PLCL1"
##
## $blue
## [1] "RORA" "SOS1" "RBMS1" "RUNX2" "PLCB1" "ZSWIM5"
## [7] "ELOVL6" "CNNM2" "PDE4D" "MYBL1" "CR1" "SNTG2"
## [13] "ABCB1" "LINC00299" "FRY" "B4GALT5" "TRIQK" "TNFAIP3"
## [19] "DST" "MTUS2"
##
## $black
## [1] "BANK1" "LYN" "ZEB2" "AFF3" "EBF1" "VCAN" "IGKC" "SETBP1"
## [9] "AOAH" "MAP3K8" "GRK3" "PLXDC2" "SKAP2" "UBE2E2" "ALOX5" "DMXL2"
## [17] "CCSER1" "TRIO" "MAML3" "TCF7L2"
##
## $yellow
## [1] "RPS23" "RPLP1" "RPL28" "RPS18" "RPL13" "RPLP2" "RPS2" "RPL3"
## [9] "TMSB10" "RPS19" "RPS28" "EEF1A1" "RPL18" "TRBC1" "TRBC2" "ID2"
##
## $green
## [1] "C1orf21" "GTDC1" "DTHD1" "PDGFD" "TGFBR3" "GAS7"
## [7] "KLRK1" "SAMD3" "LINC02384" "PPP2R2B" "NCALD" "SYTL2"
## [13] "MCTP2"
##
## $brown
## [1] "AC013652.1" "LINC02694" "TOX" "TSHR" "CDHR3"
## [6] "TTN" "IKZF2" "CCDC141" "AC093865.1" "RTKN2"
## [11] "STAM" "IL7" "ATXN7L1" "CYTOR" "ZC2HC1A"
## [16] "XYLB" "EZH2"
##
## $red
## [1] "F5" "AL136456.1" "NTN4" "PTPN13" "DLEU1"
## [6] "CYTH3" "AL589693.1" "COL5A3" "NEDD4L" "MCF2L2"
## [11] "MAPK10" "KLF7"
##
## [1] "5014_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7275## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.2652e-15
## PC_ 1
## Positive: PARP8, PLCB1, ARHGAP26, THEMIS, PDZD8, RORA, TGFBR3, ARHGAP15, MYBL1, NCALD
## LINC01619, PPP3CA, PAM, MVB12B, NIBAN1, SIK3, LINC00299, IFNG-AS1, AF165147.1, ZEB2
## Negative: RPL13, RPL28, RPLP2, RPL41, RPS18, EEF1A1, TPT1, RPS8, RPS19, RPLP1
## RPL38, RPS2, RPS23, RPL11, RPS28, RPS12, RPL18A, RPL12, RPL36A, RPS15
## PC_ 2
## Positive: PRKCA, SERINC5, INPP4B, LEF1, TXK, GNAQ, AC139720.1, CAMK4, SESN3, MGAT5
## LDLRAD4, TSHZ2, CMTM8, ARHGAP15, PELI1, MAML2, PAG1, TIAM1, FAAH2, CSGALNACT1
## Negative: ZEB2, ARHGAP26, C1orf21, GNLY, AOAH, SETBP1, AGAP1, LINC02384, PDGFD, TGFBR3
## SYTL2, PPP2R2B, KLRD1, MVB12B, NKG7, A2M, AL392086.3, DTHD1, NCALD, EIF4G3
## PC_ 3
## Positive: TOX, IKZF2, AC093865.1, CCDC141, TTN, STAM, RTKN2, ST8SIA6, MIR181A1HG, HPGD
## VAV3, CDHR3, F5, MAP3K1, LINC02694, AC090125.1, ZEB2, ATP8A1, AC243829.2, FCRL3
## Negative: ANK3, PLCB1, IFNG-AS1, RBMS1, NR3C2, NELL2, PELI2, BCL2, MYBL1, CASC8
## RPLP2, CDC14A, A2M, TNFAIP3, PZP, ME1, RPS19, SBF2, EEF1A1, RPL13
## PC_ 4
## Positive: IFNG-AS1, UBASH3B, SERINC5, FAAH2, BTBD11, AC245060.5, ETV6, DIRC3, AL078604.4, ROR2
## PAG1, LRRC8D, CENPF, DHRSX, MKI67, FAM184A, ZBTB16, ABCB9, SLC5A11, ANK3
## Negative: RPL11, EEF1A1, RPLP2, RPS12, RPS15, RPL18A, RPS2, RPS19, RPL28, RPL13
## RPS8, RPL38, RPL41, RPS23, RPS18, RPS28, TPT1, RPL36A, RPL12, RPLP1
## PC_ 5
## Positive: KLRK1, IGF1R, TXK, AOAH, AC243829.2, AL353660.1, GFOD1, PIK3AP1, MTSS1, C1orf21
## BNC2, KLRD1, LYN, DENND5A, GNLY, EPHA1-AS1, PRKCA, BANK1, CMTM8, RALGPS2
## Negative: LINC02694, AC013652.1, HPGD, NIBAN1, AL136456.1, IL12RB2, RORA, MSC-AS1, CCR6, ZC2HC1A
## ADAM12, RBPJ, DLEU2, STAM, TNFAIP3, B4GALT5, CCDC141, PHACTR2, PAG1, NEDD4L
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 3.28e-01 -51.40000 0.8680 114.0000 1.14e+02 117.000
## 2 2 1.40e-01 -11.90000 0.8450 58.1000 5.81e+01 61.400
## 3 3 2.28e-01 -7.75000 0.3280 29.9000 2.98e+01 33.400
## 4 4 5.77e-01 -8.14000 0.4570 15.6000 1.54e+01 19.600
## 5 5 4.94e-01 -5.86000 0.4880 8.2400 8.00e+00 12.300
## 6 6 4.45e-01 -4.18000 0.6190 4.4300 4.20e+00 8.200
## 7 7 4.39e-01 -3.15000 0.7240 2.4400 2.22e+00 5.770
## 8 8 3.96e-02 -2.44000 0.1020 1.3700 1.18e+00 4.250
## 9 9 1.22e-02 -1.46000 0.2130 0.7980 6.37e-01 3.230
## 10 10 1.84e-02 -1.13000 0.0816 0.4800 3.43e-01 2.520
## 11 12 5.32e-05 -0.06230 0.2180 0.1950 1.03e-01 1.590
## 12 14 1.86e-02 0.96900 0.1890 0.0912 3.21e-02 1.040
## 13 16 4.50e-06 0.00976 0.0175 0.0480 1.01e-02 0.685
## 14 18 3.28e-03 -0.23100 0.0281 0.0274 3.32e-03 0.456
## 15 20 9.28e-03 -0.35000 -0.0184 0.0163 1.07e-03 0.305
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 1 2 3 4 5 6 7 8 9 10
## 49 25 23 23 22 21 20 18 14 12
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 10 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.## $brown
## [1] "PARP8" "PLCB1" "ARHGAP26" "THEMIS" "PDZD8"
## [6] "RORA" "MYBL1" "PPP3CA" "PAM" "NIBAN1"
## [11] "SIK3" "LINC00299" "IFNG-AS1" "AF165147.1" "SFMBT2"
## [16] "IL18RAP" "GTDC1" "SBF2" "TANC2" "B4GALT5"
## [21] "SLC4A10" "COLQ" "TPRG1"
##
## $turquoise
## [1] "TGFBR3" "NCALD" "LINC01619" "MVB12B" "ZEB2"
## [6] "SYTL2" "PPP2R2B" "C1orf21" "GNLY" "AOAH"
## [11] "SETBP1" "AGAP1" "LINC02384" "PDGFD" "KLRD1"
## [16] "NKG7" "A2M" "AL392086.3" "DTHD1" "EIF4G3"
## [21] "AC243829.2" "KLRF1" "YES1" "CEP78" "ST8SIA6"
## [26] "ATP8A1" "KLRK1" "TNFAIP3" "PZP" "CFH"
## [31] "BTBD11" "HIP1" "MBNL1" "GFOD1" "PIK3AP1"
## [36] "MTSS1" "BNC2" "LYN" "SGCD" "PPM1L"
## [41] "KLRC4" "DLEU2" "PHACTR2" "ATF7IP2" "LRIG1"
## [46] "NEAT1" "TAFA1" "KIAA0825" "ERI1"
##
## $blue
## [1] "ARHGAP15" "PRKCA" "SERINC5" "INPP4B" "CAMK4"
## [6] "MGAT5" "LDLRAD4" "PELI1" "MAML2" "PAG1"
## [11] "FAAH2" "MYO16" "SSBP2" "CDC14A" "FMN1"
## [16] "ANK3" "RBMS1" "NR3C2" "NELL2" "BCL2"
## [21] "UBASH3B" "ETV6" "DIRC3" "AL078604.4" "LRRC8D"
## [26] "ZBTB16" "SLC5A11" "AC104170.1" "BACH2" "AL136456.1"
## [31] "CCR6" "ADAM12" "MCF2L2" "GCNT4" "ST8SIA1"
## [36] "FRY" "ADAM19" "PTPN13" "RUNX2" "ELOVL4"
## [41] "SAMD12" "SNX9" "RNF19A"
##
## $yellow
## [1] "RPL13" "RPL28" "RPLP2" "RPL41" "RPS18" "EEF1A1" "TPT1" "RPS8"
## [9] "RPS19" "RPLP1" "RPL38" "RPS2" "RPS23" "RPL11" "RPS28" "RPS12"
## [17] "RPL18A" "RPL12" "RPL36A" "RPS15" "JUN" "JUNB" "PLCG2"
##
## $magenta
## [1] "TSHZ2" "AL109930.1" "LEF1" "TXK" "AC139720.1"
## [6] "SESN3" "CMTM8" "PHEX" "IGF1R" "AL353660.1"
## [11] "DENND5A" "EPHA1-AS1" "AL589693.1" "SLC22A23"
##
## $red
## [1] "PLCL1" "TOX" "IKZF2" "AC093865.1" "CCDC141"
## [6] "TTN" "STAM" "RTKN2" "VAV3" "F5"
## [11] "AC090125.1" "FCRL3" "AC245060.5" "CENPF" "MKI67"
## [16] "FAM184A" "TAFA2" "RBMS3" "CDK14" "SGPP2"
## [21] "AP002383.2"
##
## $purple
## [1] "GNAQ" "TIAM1" "CSGALNACT1" "MAP3K1" "SNED1"
## [6] "DHRSX" "USP46" "PKIA" "LINC01362" "SEMA5A"
## [11] "EGLN3" "LINC00511"
##
## $black
## [1] "MIR181A1HG" "HPGD" "CDHR3" "LINC02694" "ROR2"
## [6] "ABCB9" "BANK1" "RALGPS2" "LARGE1" "AC013652.1"
## [11] "MSC-AS1" "ZC2HC1A" "NEDD4L" "MAF" "AFF3"
## [16] "WDFY4" "OSBPL10" "IGKC" "ARHGAP24" "BLK"
##
## $green
## [1] "MIR4435-2HG" "PELI2" "CASC8" "ME1" "SLC16A1-AS1"
## [6] "IL12RB2" "RBPJ" "RGS1" "CENPE" "TBXAS1"
## [11] "TLE1" "PTPRM" "TANC1" "LINC01146" "ATP1B1"
## [16] "MIR31HG" "LINC00944" "ZNF365" "ADAM22" "ANXA1"
## [21] "AC011997.1" "PACSIN1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "638/10000 permutations failed the Mann-Whitney test."
## [1] "1159/10000 permutations failed the Mann-Whitney test."
## [1] "6471/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "PARP8" "PLCB1" "ARHGAP26" "THEMIS" "PDZD8"
## [6] "RORA" "MYBL1" "PPP3CA" "PAM" "NIBAN1"
## [11] "SIK3" "LINC00299" "IFNG-AS1" "AF165147.1" "SFMBT2"
## [16] "IL18RAP" "GTDC1" "SBF2" "TANC2" "B4GALT5"
## [21] "SLC4A10" "COLQ" "TPRG1"
##
## $turquoise
## [1] "TGFBR3" "NCALD" "LINC01619" "MVB12B" "ZEB2"
## [6] "SYTL2" "PPP2R2B" "C1orf21" "GNLY" "AOAH"
## [11] "SETBP1" "AGAP1" "LINC02384" "PDGFD" "KLRD1"
## [16] "NKG7" "A2M" "AL392086.3" "DTHD1" "EIF4G3"
## [21] "AC243829.2" "KLRF1" "YES1" "CEP78" "ST8SIA6"
## [26] "ATP8A1" "KLRK1" "TNFAIP3" "PZP" "CFH"
## [31] "BTBD11" "HIP1" "MBNL1" "GFOD1" "PIK3AP1"
## [36] "MTSS1" "BNC2" "LYN" "SGCD" "PPM1L"
## [41] "KLRC4" "DLEU2" "PHACTR2" "ATF7IP2" "LRIG1"
## [46] "NEAT1" "TAFA1" "KIAA0825" "ERI1"
##
## $blue
## [1] "ARHGAP15" "PRKCA" "SERINC5" "INPP4B" "CAMK4"
## [6] "MGAT5" "LDLRAD4" "PELI1" "MAML2" "PAG1"
## [11] "FAAH2" "MYO16" "SSBP2" "CDC14A" "FMN1"
## [16] "ANK3" "RBMS1" "NR3C2" "NELL2" "BCL2"
## [21] "UBASH3B" "ETV6" "DIRC3" "AL078604.4" "LRRC8D"
## [26] "ZBTB16" "SLC5A11" "AC104170.1" "BACH2" "AL136456.1"
## [31] "CCR6" "ADAM12" "MCF2L2" "GCNT4" "ST8SIA1"
## [36] "FRY" "ADAM19" "PTPN13" "RUNX2" "ELOVL4"
## [41] "SAMD12" "SNX9" "RNF19A"
##
## $yellow
## [1] "RPL13" "RPL28" "RPLP2" "RPL41" "RPS18" "EEF1A1" "TPT1" "RPS8"
## [9] "RPS19" "RPLP1" "RPL38" "RPS2" "RPS23" "RPL11" "RPS28" "RPS12"
## [17] "RPL18A" "RPL12" "RPL36A" "RPS15" "JUN" "JUNB" "PLCG2"
##
## $magenta
## [1] "TSHZ2" "AL109930.1" "LEF1" "TXK" "AC139720.1"
## [6] "SESN3" "CMTM8" "PHEX" "IGF1R" "AL353660.1"
## [11] "DENND5A" "EPHA1-AS1" "AL589693.1" "SLC22A23"
##
## $red
## [1] "PLCL1" "TOX" "IKZF2" "AC093865.1" "CCDC141"
## [6] "TTN" "STAM" "RTKN2" "VAV3" "F5"
## [11] "AC090125.1" "FCRL3" "AC245060.5" "CENPF" "MKI67"
## [16] "FAM184A" "TAFA2" "RBMS3" "CDK14" "SGPP2"
## [21] "AP002383.2"
##
## [1] "5017_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4134## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49961## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.8439e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, THEMIS, ANK3, INPP4B, ANKRD44, ADAM19, SERINC5, PATJ, PAG1, SIK3
## RIPOR2, RORA, FMN1, FOXP1, SOS1, XKR6, PDE7A, AKT3, KLF12, MYBL1
## Negative: B2M, RPLP2, RPL13, RPS19, HLA-A, RPS27, IL32, TMSB10, ACTG1, CD52
## LTB, TPT1, S100A4, IKZF2, JUN, JUNB, TRAC, CD74, FOS, TRBC1
## PC_ 2
## Positive: NKG7, KLRD1, CCL5, ZEB2, GNLY, KLRK1, KLRC2, PPP2R2B, AC243829.2, EPB41L4A
## PRF1, GZMH, SGCD, TGFBR3, DTHD1, GZMB, GZMA, ARHGAP26, PLEK, AOAH
## Negative: LEF1, FHIT, LTB, SERINC5, ANK3, PRKCA, FAM13A, TSHZ2, MAP3K1, SESN3
## CMTM8, TPT1, PCSK5, MAML2, ALPK1, TRABD2A, FAAH2, NELL2, RPL13, MLLT3
## PC_ 3
## Positive: ANK3, AOAH, SNTB1, ZEB2, NKG7, THEMIS, CCL5, SETBP1, GNLY, NELL2
## APBA2, PLCB1, KLRD1, NR3C2, GZMH, IFNG-AS1, A2M, EPB41L4A, MCOLN2, AC243829.2
## Negative: LINC02694, STAM, AC013652.1, IKZF2, CCDC141, IL2RA, ITGB1, AC093865.1, AL136456.1, MIR181A1HG
## NIBAN1, TTN, ZC3H12C, CASK, RTKN2, SGMS1, CDK14, DUSP4, TSHR, S100A4
## PC_ 4
## Positive: MKI67, KIAA0825, KIF11, AHNAK, CHST11, CENPF, ASPM, AC105402.3, SLC16A10, LINC02725
## CIP2A, POC1A, CENPE, INCENP, ZSWIM5, TOP2A, CEP128, CDCA2, APOLD1, RGL1
## Negative: B2M, HLA-A, RPL13, LTB, FOSB, RPS19, RPLP2, RPS27, TPT1, JUNB
## PCSK5, JUN, PLCG2, IL32, MBNL1, TXK, PLXNA4, ACTG1, FAM13A, TMSB10
## PC_ 5
## Positive: ZNF365, SEMA5A, RUNX2, PRKX, TGFBR3, ADAM19, FRY, GATA3, PPARG, LINC02694
## INPP4B, VEZT, CSGALNACT1, SCCPDH, KIAA0825, FOSB, AC013652.1, JUN, LGALS3, EGLN3
## Negative: TXK, VAV3, SMG9, LINC01727, CDK14, PLCL1, FRS2, TRPS1, LARGE1, DIAPH3
## CD79A, RBM7, RALGPS2, KIF13A, ITGA4, ZSWIM6, ARHGAP24, SLC8A1, SYK, CD86
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.490 -39.40 0.9330 128.0000 1.27e+02 134.000
## 2 2 0.439 -16.20 0.9340 65.6000 6.56e+01 72.500
## 3 3 0.412 -9.11 0.8100 34.3000 3.41e+01 40.000
## 4 4 0.520 -6.62 0.8570 18.2000 1.80e+01 23.200
## 5 5 0.681 -5.82 0.9180 9.7900 9.62e+00 14.000
## 6 6 0.804 -5.19 0.9590 5.3800 5.17e+00 8.910
## 7 7 0.889 -4.18 0.9590 3.0200 2.81e+00 5.910
## 8 8 0.926 -3.43 0.9600 1.7400 1.55e+00 4.090
## 9 9 0.813 -3.00 0.7620 1.0300 8.71e-01 2.930
## 10 10 0.879 -2.48 0.8480 0.6300 4.92e-01 2.180
## 11 12 0.952 -2.04 0.9400 0.2590 1.65e-01 1.520
## 12 14 0.263 -3.11 0.0630 0.1220 5.98e-02 1.240
## 13 16 0.236 -2.49 0.0183 0.0658 2.22e-02 1.080
## 14 18 0.217 -3.12 0.0179 0.0395 8.59e-03 0.955
## 15 20 0.234 -2.95 0.0309 0.0260 3.46e-03 0.861
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7
## 123 28 26 22 21 12 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.## $green
## [1] "ARHGAP15" "THEMIS" "ADAM19" "PATJ" "FMN1" "SOS1"
## [7] "AKT3" "MYBL1" "CATSPERB" "CRYBG1" "KIAA0825" "PRKX"
##
## $black
## [1] "ANKRD44" "SIK3" "RORA" "SLC9A9" "MCOLN2" "RABGAP1L"
## [7] "XYLT1" "SKAP1" "AOPEP" "SYNE1"
##
## $red
## [1] "PAG1" "RIPOR2" "FOXP1" "PDE7A" "MAML2" "FAAH2" "MLLT3"
## [8] "RETREG1" "MBNL1" "ZBTB20"
##
## $brown
## [1] "B2M" "RPLP2" "RPL13" "RPS19" "HLA-A"
## [6] "RPS27" "IL32" "TMSB10" "ACTG1" "CD52"
## [11] "LTB" "TPT1" "S100A4" "JUN" "JUNB"
## [16] "TRAC" "FOS" "TRBC1" "AC022217.3" "DUSP1"
## [21] "FOSB" "LINC00910"
##
## $yellow
## [1] "CD74" "HLA-DRB1" "LRMDA" "AC105402.3" "SMG9"
## [6] "LARGE1" "CD79A" "RBM7" "RALGPS2" "KIF13A"
## [11] "SLC8A1" "SYK" "CD86" "UBE2E2" "CYBB"
## [16] "PRKY" "UTY" "DDX3Y" "AC114763.1" "HLA-DQB1"
## [21] "LINC00278"
##
## $blue
## [1] "NKG7" "KLRD1" "CCL5" "ZEB2" "GNLY"
## [6] "KLRK1" "KLRC2" "PPP2R2B" "AC243829.2" "EPB41L4A"
## [11] "PRF1" "GZMH" "SGCD" "TGFBR3" "DTHD1"
## [16] "GZMB" "GZMA" "ARHGAP26" "PLEK" "AOAH"
## [21] "PTGDR" "KLRC3" "IFNG" "A2M" "AC026470.2"
## [26] "KLRC4"
##
## $turquoise
## [1] "MKI67" "KIF11" "CENPF" "ASPM" "LINC02725"
## [6] "CIP2A" "POC1A" "CENPE" "INCENP" "CDCA2"
## [11] "RGL1" "MELK" "DIAPH3" "AC104850.2" "NEIL3"
## [16] "SGO2" "KNL1" "E2F2" "POLQ" "FBXO43"
## [21] "PHGDH" "BUB1B" "DTL" "PDZD2" "LIN9"
## [26] "CCNB2" "CEP152" "TMEM44"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "49/10000 permutations failed the Mann-Whitney test."
## [1] "590/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $green
## [1] "ARHGAP15" "THEMIS" "ADAM19" "PATJ" "FMN1" "SOS1"
## [7] "AKT3" "MYBL1" "CATSPERB" "CRYBG1" "KIAA0825" "PRKX"
##
## $black
## [1] "ANKRD44" "SIK3" "RORA" "SLC9A9" "MCOLN2" "RABGAP1L"
## [7] "XYLT1" "SKAP1" "AOPEP" "SYNE1"
##
## $brown
## [1] "B2M" "RPLP2" "RPL13" "RPS19" "HLA-A"
## [6] "RPS27" "IL32" "TMSB10" "ACTG1" "CD52"
## [11] "LTB" "TPT1" "S100A4" "JUN" "JUNB"
## [16] "TRAC" "FOS" "TRBC1" "AC022217.3" "DUSP1"
## [21] "FOSB" "LINC00910"
##
## $yellow
## [1] "CD74" "HLA-DRB1" "LRMDA" "AC105402.3" "SMG9"
## [6] "LARGE1" "CD79A" "RBM7" "RALGPS2" "KIF13A"
## [11] "SLC8A1" "SYK" "CD86" "UBE2E2" "CYBB"
## [16] "PRKY" "UTY" "DDX3Y" "AC114763.1" "HLA-DQB1"
## [21] "LINC00278"
##
## $blue
## [1] "NKG7" "KLRD1" "CCL5" "ZEB2" "GNLY"
## [6] "KLRK1" "KLRC2" "PPP2R2B" "AC243829.2" "EPB41L4A"
## [11] "PRF1" "GZMH" "SGCD" "TGFBR3" "DTHD1"
## [16] "GZMB" "GZMA" "ARHGAP26" "PLEK" "AOAH"
## [21] "PTGDR" "KLRC3" "IFNG" "A2M" "AC026470.2"
## [26] "KLRC4"
##
## $turquoise
## [1] "MKI67" "KIF11" "CENPF" "ASPM" "LINC02725"
## [6] "CIP2A" "POC1A" "CENPE" "INCENP" "CDCA2"
## [11] "RGL1" "MELK" "DIAPH3" "AC104850.2" "NEIL3"
## [16] "SGO2" "KNL1" "E2F2" "POLQ" "FBXO43"
## [21] "PHGDH" "BUB1B" "DTL" "PDZD2" "LIN9"
## [26] "CCNB2" "CEP152" "TMEM44"
##
## [1] "5017_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6196## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.7337e-16
## PC_ 1
## Positive: RPL41, RPS19, B2M, JUN, TRBC1, FOS, FOSB, AC103591.3, TTN, CLNK
## AP000787.1, AFF3, PPP1R15A, CROCC, SLC16A10, IER2, NEBL, TEX14, CCDC141, IKZF2
## Negative: ARHGAP15, LINC01619, PARP8, FYN, STAT4, INPP4B, PPP3CA, ZBTB20, RPS6KA3, SIK3
## ADAM19, ANK3, PAG1, SOS1, MBNL1, TC2N, CDC14A, THEMIS, RORA, PDE4B
## PC_ 2
## Positive: ANK3, TC2N, NELL2, INPP4B, FMN1, FKBP5, IFNG-AS1, TGFBR2, APBA2, PRKCA
## PITPNC1, ADAM19, ITGA4, BTBD11, THEMIS, BACH2, RASGRF2, MCOLN2, A2M, PELI2
## Negative: IKZF2, AC093865.1, LINC02694, AL136456.1, STAM, HPGD, IL2RA, TOX, ENTPD1, CCDC141
## TTN, MIR181A1HG, CDHR3, AC013652.1, CASK, RTKN2, VAV3, ZC2HC1A, NIBAN1, AC011997.1
## PC_ 3
## Positive: AOAH, ZEB2, ARHGAP26, IL18RAP, C1orf21, DTHD1, SYTL3, MVB12B, PPP2R2B, IFNG-AS1
## GNLY, SAMD3, CCL5, PLCB1, TGFBR3, AGAP1, SYTL2, GZMH, CHST11, AF165147.1
## Negative: FHIT, SESN3, FAM13A, PRKCA, TSHZ2, AP000787.1, PLCL1, PLCG2, B2M, IMMP2L
## AFF3, AL109930.1, TAFA2, MBNL1, SPON1, PLXNA4, RETREG1, CMTM8, ZBTB20, BCL2
## PC_ 4
## Positive: ATP8B4, ADAM28, C1orf21, TCF4, HDAC9, PLCB1, TRIO, MAML3, AUTS2, ANGPT1
## ZRANB2-AS2, PIP5K1B, SPOCK3, PRKG1, MED12L, PHACTR1, FLT1, MAGI2, ZEB2, VWDE
## Negative: CENPF, SGO2, KIF15, NCAPG, RRM2, KIF14, KIF18B, CDCA2, DLGAP5, PRR11
## MKI67, ASPM, BUB1, CENPE, BUB1B, POLQ, KIF18A, CCNB2, CDK1, CIT
## PC_ 5
## Positive: SNED1, LINC02694, AC013652.1, NIBAN1, CSGALNACT1, ADAM19, SEMA5A, SYTL3, PAG1, GAB2
## CDHR3, CAMK4, PPP1R16B, IL2RA, KAT2B, RUNX2, ERN1, TGFBR3, TIAM1, AC005237.1
## Negative: KIF15, RRM2, CENPF, DLGAP5, GPC5, KIF18B, KIF14, CDCA2, SGO2, PRR11
## ASPM, NRIP1, CD38, KLHL13, NUSAP1, NCAPG, KIF18A, ATP8B4, PIP5K1B, CASC15
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.0655 12.30 0.9170 130.0000 1.30e+02 135.00
## 2 2 0.0034 1.12 0.9020 67.1000 6.70e+01 72.60
## 3 3 0.3010 -7.40 0.7100 34.8000 3.47e+01 40.90
## 4 4 0.5480 -7.96 0.6180 18.2000 1.80e+01 24.30
## 5 5 0.6500 -6.48 0.5610 9.6500 9.46e+00 15.50
## 6 6 0.7390 -5.40 0.6810 5.1800 5.00e+00 10.60
## 7 7 0.2750 -9.72 0.0879 2.8300 2.67e+00 7.74
## 8 8 0.2890 -7.77 0.1070 1.5800 1.44e+00 6.02
## 9 9 0.2290 -5.66 0.0393 0.9050 7.89e-01 4.91
## 10 10 0.1180 -2.58 0.1060 0.5360 4.32e-01 4.16
## 11 12 0.1450 -2.83 -0.0079 0.2130 1.34e-01 3.21
## 12 14 0.1470 -2.62 -0.0213 0.1030 4.29e-02 2.63
## 13 16 0.1640 -2.42 -0.0249 0.0610 1.40e-02 2.23
## 14 18 0.2560 -2.65 0.0437 0.0418 4.59e-03 1.94
## 15 20 0.1570 -2.10 -0.0302 0.0315 1.55e-03 1.71
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8
## 131 27 26 16 14 11 11 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 7 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 7 module eigengenes in given set.## $red
## [1] "LINC01619" "PPP3CA" "PAG1" "NIBAN1" "SYTL3" "SAMD3"
## [7] "SYTL2" "CHST11" "TPRG1" "PPP1R16B" "KAT2B"
##
## $green
## [1] "PARP8" "FYN" "STAT4" "INPP4B" "ZBTB20"
## [6] "SIK3" "ANK3" "MBNL1" "TC2N" "THEMIS"
## [11] "PDE4B" "ATP8A1" "CBLB" "TGFBR3" "NELL2"
## [16] "FKBP5" "IFNG-AS1" "TGFBR2" "APBA2" "PITPNC1"
## [21] "BTBD11" "BACH2" "RASGRF2" "MCOLN2" "A2M"
## [26] "PZP" "DPP4" "CYTH1" "SBF2" "BCL2"
## [31] "AC139720.1" "CNOT6L" "PCSK5" "MYBL1" "SLC9A9"
##
## $black
## [1] "LINC02694" "HPGD" "CDHR3" "AC013652.1" "AC011997.1"
## [6] "ST8SIA6" "GLCCI1" "CD247" "IPCEF1" "LDLRAD4"
##
## $brown
## [1] "AOAH" "ZEB2" "ARHGAP26" "IL18RAP" "C1orf21" "DTHD1"
## [7] "MVB12B" "PPP2R2B" "GNLY" "CCL5" "PLCB1" "GZMH"
## [13] "KLRD1" "SLC4A4" "EPB41L4A" "MCTP2"
##
## $turquoise
## [1] "ATP8B4" "ADAM28" "TCF4" "MAML3" "ANGPT1"
## [6] "ZRANB2-AS2" "PIP5K1B" "SPOCK3" "PRKG1" "MED12L"
## [11] "PHACTR1" "FLT1" "MAGI2" "VWDE" "THRB"
## [16] "AC092164.1" "LINC01122" "B4GALT6" "NKAIN2" "GPC5"
## [21] "NRIP1" "KLHL13" "CASC15" "PPM1F" "AL355612.1"
## [26] "CYSLTR2" "DOCK5"
##
## $blue
## [1] "CENPF" "SGO2" "KIF15" "NCAPG" "RRM2" "KIF14" "KIF18B" "CDCA2"
## [9] "DLGAP5" "PRR11" "MKI67" "ASPM" "BUB1" "CENPE" "BUB1B" "POLQ"
## [17] "KIF18A" "CCNB2" "CDK1" "CIT" "DIAPH3" "KNL1" "TOP2A" "CDCA8"
## [25] "SGO1" "NUSAP1"
##
## [1] "69/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $red
## [1] "LINC01619" "PPP3CA" "PAG1" "NIBAN1" "SYTL3" "SAMD3"
## [7] "SYTL2" "CHST11" "TPRG1" "PPP1R16B" "KAT2B"
##
## $green
## [1] "PARP8" "FYN" "STAT4" "INPP4B" "ZBTB20"
## [6] "SIK3" "ANK3" "MBNL1" "TC2N" "THEMIS"
## [11] "PDE4B" "ATP8A1" "CBLB" "TGFBR3" "NELL2"
## [16] "FKBP5" "IFNG-AS1" "TGFBR2" "APBA2" "PITPNC1"
## [21] "BTBD11" "BACH2" "RASGRF2" "MCOLN2" "A2M"
## [26] "PZP" "DPP4" "CYTH1" "SBF2" "BCL2"
## [31] "AC139720.1" "CNOT6L" "PCSK5" "MYBL1" "SLC9A9"
##
## $black
## [1] "LINC02694" "HPGD" "CDHR3" "AC013652.1" "AC011997.1"
## [6] "ST8SIA6" "GLCCI1" "CD247" "IPCEF1" "LDLRAD4"
##
## $brown
## [1] "AOAH" "ZEB2" "ARHGAP26" "IL18RAP" "C1orf21" "DTHD1"
## [7] "MVB12B" "PPP2R2B" "GNLY" "CCL5" "PLCB1" "GZMH"
## [13] "KLRD1" "SLC4A4" "EPB41L4A" "MCTP2"
##
## $turquoise
## [1] "ATP8B4" "ADAM28" "TCF4" "MAML3" "ANGPT1"
## [6] "ZRANB2-AS2" "PIP5K1B" "SPOCK3" "PRKG1" "MED12L"
## [11] "PHACTR1" "FLT1" "MAGI2" "VWDE" "THRB"
## [16] "AC092164.1" "LINC01122" "B4GALT6" "NKAIN2" "GPC5"
## [21] "NRIP1" "KLHL13" "CASC15" "PPM1F" "AL355612.1"
## [26] "CYSLTR2" "DOCK5"
##
## $blue
## [1] "CENPF" "SGO2" "KIF15" "NCAPG" "RRM2" "KIF14" "KIF18B" "CDCA2"
## [9] "DLGAP5" "PRR11" "MKI67" "ASPM" "BUB1" "CENPE" "BUB1B" "POLQ"
## [17] "KIF18A" "CCNB2" "CDK1" "CIT" "DIAPH3" "KNL1" "TOP2A" "CDCA8"
## [25] "SGO1" "NUSAP1"
##
## [1] "5023_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5512## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50073## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.8809e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, MBNL1, DPYD, DOCK10, PAG1, CDC14A, MDFIC, CD96, RBMS1, GPRIN3
## INPP4B, RORA, STAT4, ZBTB20, STT3B, AFF1, KLHL5, THEMIS, KLF12, NFKB1
## Negative: RPL41, RPLP2, RPL13, RPL19, RPLP1, RPS28, RPL27A, RPL28, BANK1, RPS2
## RPS18, RPS15, ZEB2, RPL13A, PTK2, HLA-DRA, ARHGAP24, RPL37, RPS12, RPL11
## PC_ 2
## Positive: LINC02694, IKZF2, CCDC141, TOX, STAM, AC093865.1, CDHR3, AC013652.1, TTN, RTKN2
## MIR181A1HG, DUSP10, ATXN7L1, ZC2HC1A, SNED1, AC011997.1, LDLRAD4, CEP128, PALM2-AKAP2, SLC1A4
## Negative: ANK3, THEMIS, ITGA4, BACH2, NELL2, PRKCA, NR3C2, PDE4D, SBF2, RBMS1
## PRKN, PELI2, MYBL1, ADAM23, PLCB1, INPP4B, STAT4, CDK6, UST, DPP4
## PC_ 3
## Positive: SLC16A1-AS1, SKAP1, CORO2A, FOXP1, SPPL3, FUT10, BTBD11, MB21D2, ATF7, ACYP2
## ANXA4, TMEM182, EFCAB5, GLUD1, TTN, NINJ2, CUBN, ABHD3, DRAM1, DLGAP1
## Negative: RPL11, RPS19, RPS2, RPL3, RPL18A, AC079793.1, RPL13, RPL28, RPLP2, RPL38
## RPS15, TPT1, RPL13A, RPL19, EEF1A1, RPL23, RPLP1, RPS18, RPS28, RPL27A
## PC_ 4
## Positive: RPL38, PRKCA, RPL27A, TRBC1, TMSB10, PLCL1, RPS2, LEF1, TPT1, EEF1A1
## KANK1, INPP4B, RPL13A, RPL28, TRAT1, IL32, RPS18, RPL37, CRIP1, TSHZ2
## Negative: TBC1D9, CDK14, SETBP1, EBF1, BANK1, LYN, OSBPL10, TCF4, ZEB2, JCHAIN
## MS4A1, AFF3, HDAC9, IGKC, LRRK2, ARHGAP24, MEF2C, HLA-DQA1, FCRL1, STK33
## PC_ 5
## Positive: PLCB1, LINC00299, ABCB1, SLC4A10, LINC01644, PPP2R2B, NCALD, SAMD3, SYTL2, PDGFD
## MYBL1, RUNX2, PDE4D, AL136456.1, TMCC3, AGAP1, NTN4, ADAM12, NEDD4, IL12RB2
## Negative: TSHZ2, FHIT, SESN3, ESR1, LEF1, JAM3, CDK14, TBC1D9, FAAH2, TRIO
## APP, IL6ST, JCHAIN, AC139720.1, CERS6, USP6NL, LINC01362, RALGPS2, AL353660.1, KCNQ5
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00879 3.260 0.8980 116.0000 1.16e+02 124.000
## 2 2 0.00183 -0.698 0.9080 60.3000 6.02e+01 69.000
## 3 3 0.02490 -1.690 0.9600 31.9000 3.17e+01 39.100
## 4 4 0.01970 -1.060 0.9710 17.1000 1.70e+01 22.500
## 5 5 0.01460 -0.596 0.9290 9.3300 9.19e+00 13.100
## 6 6 0.07400 -0.805 0.8310 5.1900 4.98e+00 7.930
## 7 7 0.29500 -1.340 0.8970 2.9500 2.76e+00 5.230
## 8 8 0.59200 -1.660 0.8450 1.7200 1.54e+00 3.570
## 9 9 0.77700 -1.780 0.8880 1.0200 8.73e-01 2.510
## 10 10 0.88700 -1.740 0.9250 0.6240 5.03e-01 1.800
## 11 12 0.93500 -1.550 0.9210 0.2510 1.72e-01 0.978
## 12 14 0.94800 -1.420 0.9330 0.1110 6.12e-02 0.553
## 13 16 0.22200 -2.890 0.0866 0.0536 2.29e-02 0.320
## 14 18 0.79900 -1.270 0.7440 0.0277 9.01e-03 0.210
## 15 20 0.23200 -2.390 0.1270 0.0151 3.49e-03 0.145
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3
## 178 26 11 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $brown
## [1] "ARHGAP15" "DOCK10" "MDFIC" "RBMS1" "INPP4B" "ZBTB20"
## [7] "STT3B" "NFKB1" "PRKCA" "NR3C2" "BCL2"
##
## $turquoise
## [1] "RPL41" "RPLP2" "RPL13" "RPL19" "RPLP1" "RPS28" "RPL27A" "RPL28"
## [9] "RPS2" "RPS18" "RPS15" "RPL13A" "RPL37" "RPS12" "RPL11" "RPS19"
## [17] "RPL18A" "TMSB10" "RPL38" "RPL3" "TPT1" "EEF1A1" "RPL23" "FAU"
## [25] "TRBC1" "IL32"
##
## $blue
## [1] "LINC02694" "IKZF2" "CCDC141" "TOX" "STAM"
## [6] "AC093865.1" "CDHR3" "AC013652.1" "TTN" "DUSP10"
## [11] "AC011997.1"
##
## [1] "5/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "ARHGAP15" "DOCK10" "MDFIC" "RBMS1" "INPP4B" "ZBTB20"
## [7] "STT3B" "NFKB1" "PRKCA" "NR3C2" "BCL2"
##
## $turquoise
## [1] "RPL41" "RPLP2" "RPL13" "RPL19" "RPLP1" "RPS28" "RPL27A" "RPL28"
## [9] "RPS2" "RPS18" "RPS15" "RPL13A" "RPL37" "RPS12" "RPL11" "RPS19"
## [17] "RPL18A" "TMSB10" "RPL38" "RPL3" "TPT1" "EEF1A1" "RPL23" "FAU"
## [25] "TRBC1" "IL32"
##
## $blue
## [1] "LINC02694" "IKZF2" "CCDC141" "TOX" "STAM"
## [6] "AC093865.1" "CDHR3" "AC013652.1" "TTN" "DUSP10"
## [11] "AC011997.1"
##
## [1] "5021_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6384## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50169## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.1971e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ZEB2, AGAP1, TGFBR3, C1orf21, SETBP1, AOAH, LINC02384, PLCB1, MYO3B, ZFPM2
## PPP2R2B, MYBL1, LGR6, AL139383.1, MSC-AS1, MIR4435-2HG, FRMPD3, LINC00299, LYN, SLCO4C1
## Negative: INPP4B, ARHGAP15, CD28, PAG1, CDC14A, PRKCA, SERINC5, ANK3, STT3B, RBMS1
## TAB2, MBNL1, PDE3B, LEF1, DOCK10, AC139720.1, ADAM19, AC079793.1, GPRIN3, FAAH2
## PC_ 2
## Positive: ZEB2, C1orf21, TGFBR3, PARP8, RABGAP1L, JAZF1, NCALD, PPP2R2B, AGAP1, PDGFD
## CBLB, SETBP1, TOX, MIR4435-2HG, LINC02384, EIF4G3, KLRG1, GTDC1, DNAJC1, MYO3B
## Negative: TIAM1, SERINC5, LEF1, PRKCA, FAAH2, RCAN3, MB21D2, TSHZ2, TSPAN18, TCF7
## PVT1, PATJ, ADAM19, AC139720.1, BCL2, CD28, PLCL1, IL2RA, RPL13, SNED1
## PC_ 3
## Positive: DTL, POLQ, FAM111B, STMN1, RRM2, UHRF1, ORC1, NUSAP1, DIAPH3, MYBL2
## RGS12, EXO1, SHCBP1, RAD51, FANCD2, CCNE2, HHLA3, FANCA, CIT, CLSPN
## Negative: GTDC1, C1orf21, STAU2, LINC00299, RFX3-AS1, EPSTI1, FRY, MGMT, THEMIS, ARID5B
## ST8SIA6, AF165147.1, RBMS1, SLC10A7, RORA, MAP3K8, AC078845.1, TPRG1, ANGEL1, HEATR5A
## PC_ 4
## Positive: RPS6, RPS15, RPS28, RPL28, LTB, RPLP2, RPS23, EEF1A1, RPL13, RPL13A
## AC079793.1, RPS2, RPL36A, AC013652.1, RPS19, FAU, CDYL2, RPL18, RPL18A, RPL3
## Negative: RSPO4, EDA, JAM3, AP003557.1, AL589693.1, ADTRP, SUCLG2-AS1, REPS2, AKAP6, FZD6
## CUBN, PCSK5, LPAR3, IGF1R, NBEA, GLIS3, KANK1, EPHB1, PPFIBP1, BCL2L15
## PC_ 5
## Positive: AC093865.1, IKZF2, KLRC3, KLRK1, KLRC2, MTSS1, TTN, BNC2, CD8A, AC243829.2
## CD8B, ATP8B4, LYST, AOAH, PIK3AP1, FZD4-DT, FAM49A, AC104041.1, ARHGAP42, AP003557.1
## Negative: PTPRM, LINC00299, PLCB1, ANK3, THEMIS, RORA, FKBP5, MYBL1, LINC01619, NCALD
## IL12RB2, BTBD11, ADAM19, PLEKHA5, IL18R1, BCL2, IFNG-AS1, HOMER1, LINC02694, ANTXR2
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.06680 5.650 0.5090 65.4000 65.20000 69.900
## 2 2 0.17000 4.060 0.6660 34.9000 34.70000 39.500
## 3 3 0.00364 0.402 0.5770 19.0000 18.90000 23.500
## 4 4 0.07020 -1.320 0.7560 10.5000 10.60000 14.800
## 5 5 0.28500 -2.090 0.8700 5.9800 5.88000 9.860
## 6 6 0.15500 -5.380 -0.0500 3.4700 3.38000 6.890
## 7 7 0.18600 -4.820 -0.0108 2.0600 1.98000 5.020
## 8 8 0.24500 -6.440 0.0289 1.2500 1.19000 3.800
## 9 9 0.26400 -5.830 0.0540 0.7730 0.71200 2.950
## 10 10 0.28200 -5.450 0.0773 0.4900 0.42500 2.330
## 11 12 0.31800 -5.620 0.1260 0.2110 0.15900 1.530
## 12 14 0.31600 -5.030 0.1220 0.0992 0.06090 1.040
## 13 16 0.30800 -4.470 0.1110 0.0506 0.02400 0.717
## 14 18 0.28000 -4.280 0.1130 0.0278 0.00988 0.505
## 15 20 0.26900 -3.900 0.0905 0.0163 0.00420 0.360
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 1 2 3 4 5
## 41 28 27 20 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.## $turquoise
## [1] "ZEB2" "AGAP1" "TGFBR3" "C1orf21" "SETBP1"
## [6] "AOAH" "PLCB1" "MYO3B" "MYBL1" "LGR6"
## [11] "MSC-AS1" "MIR4435-2HG" "SLCO4C1" "PIP5K1B" "CTBP2"
## [16] "AC243829.2" "PARP8" "RABGAP1L" "NCALD" "CBLB"
## [21] "TOX" "EIF4G3" "KLRG1" "DNAJC1" "JAKMIP2"
## [26] "TFDP2" "RFX3-AS1" "EPSTI1" "MGMT" "ST8SIA6"
## [31] "AF165147.1" "SLC10A7" "RORA" "MAP3K8" "AC078845.1"
## [36] "TPRG1" "ANGEL1" "HEATR5A" "SETDB2" "BTBD9"
## [41] "MAP2K4"
##
## $blue
## [1] "LINC02384" "ZFPM2" "PPP2R2B" "AL139383.1" "FRMPD3"
## [6] "LINC00299" "LYN" "CLIP2" "AL365295.1" "JAZF1"
## [11] "PDGFD" "GTDC1" "THEMIS" "DTL" "POLQ"
## [16] "FAM111B" "STMN1" "RRM2" "UHRF1" "ORC1"
## [21] "NUSAP1" "DIAPH3" "MYBL2" "RGS12" "EXO1"
## [26] "SHCBP1" "RAD51" "FANCD2" "CCNE2" "HHLA3"
## [31] "FANCA" "CIT" "CLSPN" "BRIP1" "NCAPH"
## [36] "CENPK" "VAV2" "BUB1"
##
## $brown
## [1] "INPP4B" "ARHGAP15" "CD28" "PAG1" "CDC14A"
## [6] "PRKCA" "SERINC5" "ANK3" "STT3B" "RBMS1"
## [11] "TAB2" "MBNL1" "PDE3B" "LEF1" "DOCK10"
## [16] "AC139720.1" "ADAM19" "AC079793.1" "GPRIN3" "FAAH2"
## [21] "ZBTB20" "MDFIC" "PATJ" "AKT3" "PLCG2"
## [26] "TIAM1" "RCAN3" "MB21D2" "TSHZ2" "TSPAN18"
## [31] "TCF7" "PVT1" "BCL2" "PLCL1" "IL2RA"
## [36] "RPL13" "SNED1" "PLXNA4" "TXK" "KANK1"
## [41] "AL589693.1" "EDA" "STAU2" "FRY" "ARID5B"
## [46] "MALAT1" "GMDS-DT"
##
## [1] "3/10000 permutations failed the Mann-Whitney test."
## [1] "12/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "ZEB2" "AGAP1" "TGFBR3" "C1orf21" "SETBP1"
## [6] "AOAH" "PLCB1" "MYO3B" "MYBL1" "LGR6"
## [11] "MSC-AS1" "MIR4435-2HG" "SLCO4C1" "PIP5K1B" "CTBP2"
## [16] "AC243829.2" "PARP8" "RABGAP1L" "NCALD" "CBLB"
## [21] "TOX" "EIF4G3" "KLRG1" "DNAJC1" "JAKMIP2"
## [26] "TFDP2" "RFX3-AS1" "EPSTI1" "MGMT" "ST8SIA6"
## [31] "AF165147.1" "SLC10A7" "RORA" "MAP3K8" "AC078845.1"
## [36] "TPRG1" "ANGEL1" "HEATR5A" "SETDB2" "BTBD9"
## [41] "MAP2K4"
##
## $blue
## [1] "LINC02384" "ZFPM2" "PPP2R2B" "AL139383.1" "FRMPD3"
## [6] "LINC00299" "LYN" "CLIP2" "AL365295.1" "JAZF1"
## [11] "PDGFD" "GTDC1" "THEMIS" "DTL" "POLQ"
## [16] "FAM111B" "STMN1" "RRM2" "UHRF1" "ORC1"
## [21] "NUSAP1" "DIAPH3" "MYBL2" "RGS12" "EXO1"
## [26] "SHCBP1" "RAD51" "FANCD2" "CCNE2" "HHLA3"
## [31] "FANCA" "CIT" "CLSPN" "BRIP1" "NCAPH"
## [36] "CENPK" "VAV2" "BUB1"
##
## $brown
## [1] "INPP4B" "ARHGAP15" "CD28" "PAG1" "CDC14A"
## [6] "PRKCA" "SERINC5" "ANK3" "STT3B" "RBMS1"
## [11] "TAB2" "MBNL1" "PDE3B" "LEF1" "DOCK10"
## [16] "AC139720.1" "ADAM19" "AC079793.1" "GPRIN3" "FAAH2"
## [21] "ZBTB20" "MDFIC" "PATJ" "AKT3" "PLCG2"
## [26] "TIAM1" "RCAN3" "MB21D2" "TSHZ2" "TSPAN18"
## [31] "TCF7" "PVT1" "BCL2" "PLCL1" "IL2RA"
## [36] "RPL13" "SNED1" "PLXNA4" "TXK" "KANK1"
## [41] "AL589693.1" "EDA" "STAU2" "FRY" "ARID5B"
## [46] "MALAT1" "GMDS-DT"
##
## [1] "5037_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7007## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.5654e-16
## PC_ 1
## Positive: ARHGAP15, MBNL1, ZBTB20, DPYD, INPP4B, PAG1, CAMK4, RORA, AKT3, PLCL2
## ANK3, FOXP1, KLF12, RBMS1, PLCG2, MGAT5, LINC01619, TNFAIP8, FBXL17, GPRIN3
## Negative: AC105402.3, GNLY, SLA2, PPARG, RBFOX3, STPG2, CDH4, AOAH, LYN, CCBE1
## LHFPL2, RRM2, PIK3AP1, ZEB2, AC020916.1, TTC28, SDK1, GPC6, OSBPL5, LINC02267
## PC_ 2
## Positive: LEF1, TSHZ2, INPP4B, PRKCA, FHIT, AC139720.1, TXK, FAAH2, CMTM8, GNAQ
## HIVEP2, MAML2, PLCL1, RASGRF2, BCL2, NELL2, BACH2, SESN3, MAN1C1, AL589693.1
## Negative: ZEB2, C1orf21, AOAH, SYNE1, TGFBR3, CMIP, SYTL3, GNLY, CEMIP2, PPP2R2B
## LINC02384, ATP8A1, SETBP1, MVB12B, PPP1R16B, SLA2, OSBPL5, PDGFD, YES1, NCALD
## PC_ 3
## Positive: RASGRF2, A2M, ATP10A, PLCB1, TAFA1, AOAH, NELL2, C1orf21, SBF2, SAMD3
## IFNG-AS1, MCTP2, APBA2, ITGA4, AC139720.1, PCSK5, AGAP1, PRKN, GNLY, GSAP
## Negative: LINC02694, MCF2L2, ENTPD1, PLD1, STAM, PTPN13, PKIA, MIR181A1HG, AL136456.1, AC013652.1
## PELI1, ADAM12, CENPE, TANC1, TOP2A, NIBAN1, KIF20B, LDLRAD4, AC093865.1, DUSP4
## PC_ 4
## Positive: IKZF2, AC093865.1, TTN, CCDC141, RTKN2, TOX, LEF1, CDHR3, ENTPD1, SLC16A10
## STAM, JAZF1, TAFA2, SGMS1, C1orf112, ATXN7L1, VAV3, FANK1, CKAP2L, TMSB10
## Negative: FRY, PTPN13, TANC1, ADAM19, PDE4D, ANK3, MYBL1, RBMS1, LINC02649, ADAM12
## PELI2, GAB2, LINC00299, RORA, PRKCA, EML4, KLHL5, RUNX2, BCL2, BTBD11
## PC_ 5
## Positive: KIF11, KIF15, CCNA2, KIF14, CDCA8, E2F7, CENPF, SH3RF2, ECT2, MKI67
## KIF23, HJURP, RAD51AP1, KIFC1, NCAPG, CCDC150, CCNB1, CKAP2L, KIF18B, DLGAP5
## Negative: RTKN2, STAM, TOX, TTN, LINC02694, CCDC141, AC093865.1, IKZF2, AC013652.1, HPGD
## LDLRAD4, SETD7, SLC16A10, FANK1, FOXP3, TAFA2, CASK, SGMS1, PELI1, GLCCI1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00189 -1.51 0.952000 116.0000 1.16e+02 124.00
## 2 2 0.10700 -4.96 0.951000 60.2000 5.99e+01 69.10
## 3 3 0.11500 -2.84 0.914000 31.6000 3.14e+01 39.20
## 4 4 0.28500 -3.03 0.766000 16.8000 1.66e+01 22.90
## 5 5 0.47300 -3.80 0.551000 9.0100 8.79e+00 14.70
## 6 6 0.28800 -8.85 0.171000 4.9000 4.69e+00 10.10
## 7 7 0.31600 -9.49 0.125000 2.7100 2.53e+00 7.37
## 8 8 0.81500 -3.07 0.828000 1.5300 1.38e+00 5.67
## 9 9 0.17300 -3.61 0.101000 0.8820 7.52e-01 4.56
## 10 10 0.17300 -3.11 0.108000 0.5240 4.16e-01 3.79
## 11 12 0.17600 -3.18 0.035100 0.2060 1.32e-01 2.81
## 12 14 0.09390 -2.22 0.037700 0.0972 4.40e-02 2.21
## 13 16 0.17900 -2.55 -0.000718 0.0552 1.52e-02 1.82
## 14 18 0.19800 -2.30 0.001990 0.0367 5.22e-03 1.53
## 15 20 0.15100 -2.00 0.040300 0.0271 1.80e-03 1.31
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3
## 171 25 18 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "ARHGAP15" "MBNL1" "ZBTB20" "DPYD" "PAG1" "CAMK4"
## [7] "AKT3" "PLCL2" "FOXP1" "PLCG2" "MGAT5" "TNFAIP8"
## [13] "FBXL17" "GNAQ" "MDFIC" "HIVEP2" "LEF1" "MAML2"
##
## $brown
## [1] "GNLY" "SLA2" "AOAH" "ZEB2" "OSBPL5" "C1orf21" "SYNE1"
## [8] "CMIP" "SYTL3" "YES1" "ADGRE5"
##
## $turquoise
## [1] "RRM2" "TOP2A" "CKAP2L" "KIF11" "KIF15" "CCNA2"
## [7] "KIF14" "CDCA8" "E2F7" "CENPF" "SH3RF2" "ECT2"
## [13] "MKI67" "KIF23" "HJURP" "RAD51AP1" "KIFC1" "NCAPG"
## [19] "CCDC150" "CCNB1" "KIF18B" "DLGAP5" "ANLN" "POLQ"
## [25] "CCNF"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "39/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "ARHGAP15" "MBNL1" "ZBTB20" "DPYD" "PAG1" "CAMK4"
## [7] "AKT3" "PLCL2" "FOXP1" "PLCG2" "MGAT5" "TNFAIP8"
## [13] "FBXL17" "GNAQ" "MDFIC" "HIVEP2" "LEF1" "MAML2"
##
## $brown
## [1] "GNLY" "SLA2" "AOAH" "ZEB2" "OSBPL5" "C1orf21" "SYNE1"
## [8] "CMIP" "SYTL3" "YES1" "ADGRE5"
##
## $turquoise
## [1] "RRM2" "TOP2A" "CKAP2L" "KIF11" "KIF15" "CCNA2"
## [7] "KIF14" "CDCA8" "E2F7" "CENPF" "SH3RF2" "ECT2"
## [13] "MKI67" "KIF23" "HJURP" "RAD51AP1" "KIFC1" "NCAPG"
## [19] "CCDC150" "CCNB1" "KIF18B" "DLGAP5" "ANLN" "POLQ"
## [25] "CCNF"
##
## [1] "5021_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4015## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.5002## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.0303e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: CDC14A, ARHGAP15, INPP4B, CAMK4, MBNL1, PAG1, RBMS1, GPRIN3, HIVEP2, MDFIC
## LEF1, MTAP, MAP3K1, OXNAD1, SERINC5, ANK3, TNFAIP8, RORA, GNAQ, ADAM19
## Negative: ZEB2, TOX2, LYN, SETBP1, AOAH, LINC02384, C1orf21, GNLY, OSBPL5, AC243829.2
## PECAM1, PRSS23, PDGFD, AGAP1, CCL5, HULC, TCF7L2, KLRK1, DTHD1, GAS7
## PC_ 2
## Positive: SERINC5, BCL2, ADAM19, PRKCA, TIAM1, LEF1, PAG1, AC139720.1, PVT1, TSHZ2
## RCAN3, MYO16, ANK3, PLCL1, TAB2, CAMK4, AL589693.1, MAP3K1, SAMD12, RNF157
## Negative: ZEB2, TGFBR3, C1orf21, SYTL2, PPP2R2B, MYO3B, LINC02384, MYBL1, TOX, JAKMIP2
## SETBP1, RAP1B, PLCB1, JAZF1, AGAP1, TMCC3, PDGFD, NAA50, EPB41L4A, RABGAP1L
## PC_ 3
## Positive: NR3C2, ADAM23, TAFA1, SBF2, IGF1R, TANC2, PLCB1, MYBL1, PELI2, OCA2
## BCL2, C8orf37-AS1, THEMIS, BACH2, CFH, FNDC3B, EDA, EML5, CDK6, EEPD1
## Negative: ENTPD1, LINC02694, CCDC141, IL12RB2, LY96, AC011997.1, ABLIM1, DUSP4, GRK3, CCDC50
## F5, CDHR3, MIR181A1HG, LINC01727, RTKN2, AC093865.1, ATP11A, IKZF2, AC013652.1, TTN
## PC_ 4
## Positive: TBXAS1, SMAD3, FKBP5, BTBD11, PTPRM, THEMIS, ITGA4, IL18RAP, EAF1, AGPAT4
## ANK3, NCALD, ST8SIA1, PTPN13, XYLT1, TP63, RORA, TSPAN18, ECT2, NIPSNAP3A
## Negative: IKZF2, CDHR3, AC093865.1, CCDC141, SGMS1, CRYZ, AC022075.1, IL2RA, AL136441.1, RTKN2
## PLCL1, TAFA2, KLRC4, LINC01727, KLRC3, IRF4, SLC16A10, TTN, GRIP1, KLRK1
## PC_ 5
## Positive: CDIP1, MAPK3, SRGAP3, A2M, AC013652.1, ABHD15-AS1, EAF1, LSM4, AL161457.2, STRADB
## CENPI, AP002336.2, MXI1, PLCG2, ARG2, GALNT3, IPO11, LINC00612, ACVR1C, IL18RAP
## Negative: KLRC3, AC243829.2, BNC2, HPRT1, MIR181A1HG, PPM1L, DISC1FP1, GOLPH3L, SNX30, FSD1L
## TMEM156, OPHN1, CTBP2, PLXNA4, EFNA5, MTSS1, KLRC2, KLRK1, RFX8, SLC12A2
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.1960 41.900 0.0358 65.8000 65.80000 71.6000
## 2 2 0.2760 4.580 0.8040 35.3000 34.90000 41.4000
## 3 3 0.2960 2.930 0.8380 19.4000 19.10000 25.0000
## 4 4 0.1630 1.440 0.9190 10.9000 10.60000 15.6000
## 5 5 0.0131 0.289 0.8840 6.2700 5.95000 9.9700
## 6 6 0.0037 -0.112 0.8030 3.6800 3.47000 6.5100
## 7 7 0.0186 -0.213 0.7990 2.2100 2.10000 4.3200
## 8 8 0.0455 -0.308 0.6800 1.3500 1.27000 2.9100
## 9 9 0.2860 -0.795 0.6090 0.8370 0.77900 2.0200
## 10 10 0.5190 -1.130 0.7290 0.5280 0.47800 1.4800
## 11 12 0.7670 -1.480 0.8650 0.2190 0.19300 0.8130
## 12 14 0.2550 -3.490 0.1500 0.0957 0.07740 0.4600
## 13 16 0.3050 -4.560 0.2130 0.0436 0.03230 0.2660
## 14 18 0.3640 -5.520 0.2330 0.0207 0.01390 0.1570
## 15 20 0.3690 -5.280 0.2480 0.0102 0.00599 0.0947
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 26 35 30 21 15
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "CDC14A" "ARHGAP15" "INPP4B" "CAMK4" "MBNL1"
## [6] "PAG1" "RBMS1" "GPRIN3" "HIVEP2" "MDFIC"
## [11] "LEF1" "MTAP" "MAP3K1" "OXNAD1" "SERINC5"
## [16] "ANK3" "TNFAIP8" "RORA" "GNAQ" "ADAM19"
## [21] "TTC39C" "ZEB1" "TAB2" "MAML2" "PRKCA"
## [26] "BCL2" "TIAM1" "AC139720.1" "PVT1" "TSHZ2"
## [31] "RCAN3" "MYO16" "AL589693.1" "SAMD12" "RNF157"
## [36] "KCNQ1" "MB21D2" "FAAH2" "CD28" "DPP4"
## [41] "NR3C2" "ADAM23" "SBF2" "IGF1R" "PELI2"
## [46] "BACH2" "EDA" "EML5" "CDK6" "EEPD1"
## [51] "ZNF208"
##
## $turquoise
## [1] "ZEB2" "LYN" "SETBP1" "AOAH" "LINC02384"
## [6] "C1orf21" "GNLY" "OSBPL5" "AC243829.2" "PECAM1"
## [11] "PRSS23" "PDGFD" "AGAP1" "CCL5" "TCF7L2"
## [16] "KLRK1" "DTHD1" "GAS7" "TGFBR3" "EFNA5"
## [21] "EPB41L4A" "KCNQ5" "SYTL2" "PPP2R2B" "MYO3B"
## [26] "MYBL1" "TOX" "JAKMIP2" "PLCB1" "JAZF1"
## [31] "TMCC3" "NAA50" "RABGAP1L" "MCTP2" "EIF4G3"
##
## $yellow
## [1] "PLCL1" "CCDC141" "IL12RB2" "LY96" "GRK3"
## [6] "F5" "CDHR3" "MIR181A1HG" "LINC01727" "RTKN2"
## [11] "AC093865.1" "IKZF2" "TTN" "STAM" "AHRR"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "CDC14A" "ARHGAP15" "INPP4B" "CAMK4" "MBNL1"
## [6] "PAG1" "RBMS1" "GPRIN3" "HIVEP2" "MDFIC"
## [11] "LEF1" "MTAP" "MAP3K1" "OXNAD1" "SERINC5"
## [16] "ANK3" "TNFAIP8" "RORA" "GNAQ" "ADAM19"
## [21] "TTC39C" "ZEB1" "TAB2" "MAML2" "PRKCA"
## [26] "BCL2" "TIAM1" "AC139720.1" "PVT1" "TSHZ2"
## [31] "RCAN3" "MYO16" "AL589693.1" "SAMD12" "RNF157"
## [36] "KCNQ1" "MB21D2" "FAAH2" "CD28" "DPP4"
## [41] "NR3C2" "ADAM23" "SBF2" "IGF1R" "PELI2"
## [46] "BACH2" "EDA" "EML5" "CDK6" "EEPD1"
## [51] "ZNF208"
##
## $turquoise
## [1] "ZEB2" "LYN" "SETBP1" "AOAH" "LINC02384"
## [6] "C1orf21" "GNLY" "OSBPL5" "AC243829.2" "PECAM1"
## [11] "PRSS23" "PDGFD" "AGAP1" "CCL5" "TCF7L2"
## [16] "KLRK1" "DTHD1" "GAS7" "TGFBR3" "EFNA5"
## [21] "EPB41L4A" "KCNQ5" "SYTL2" "PPP2R2B" "MYO3B"
## [26] "MYBL1" "TOX" "JAKMIP2" "PLCB1" "JAZF1"
## [31] "TMCC3" "NAA50" "RABGAP1L" "MCTP2" "EIF4G3"
##
## $yellow
## [1] "PLCL1" "CCDC141" "IL12RB2" "LY96" "GRK3"
## [6] "F5" "CDHR3" "MIR181A1HG" "LINC01727" "RTKN2"
## [11] "AC093865.1" "IKZF2" "TTN" "STAM" "AHRR"
##
## [1] "5037_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7205## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50212## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.441e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: MBNL1, ARHGAP15, ZBTB20, PLCG2, INPP4B, PAG1, MAP3K1, SERINC5, RORA, CASK
## MGAT5, TBC1D5, CDC14A, STT3B, HIVEP2, ANTXR2, EXOC4, RFX3, PHACTR2, RBMS1
## Negative: GNLY, AOAH, COL25A1, AC105402.3, ZEB2, C1orf21, SETBP1, CDH4, CD300A, ADGRG5
## RBMS3, RFX2, ARHGAP26, AC243829.2, CLNK, TTC28, KLRD1, SOX5, AC034195.1, ROR2
## PC_ 2
## Positive: TSHZ2, BCL2, MAP3K1, PRKCA, AL589693.1, LEF1, ADAM19, TXK, FAAH2, KANK1
## MGAT5, CMTM8, SERINC5, AC139720.1, KLHL5, DUSP16, SAMD12, MAL, LDLRAD4, AL136456.1
## Negative: ZEB2, AOAH, TGFBR3, C1orf21, KLRD1, SAMD3, GNLY, ARHGAP26, MVB12B, PPP2R2B
## GAB3, SETBP1, OSBPL5, LINC02384, SYTL2, PDGFD, A2M, NCALD, PZP, KLRG1
## PC_ 3
## Positive: IKZF2, LINC02694, AC093865.1, CCDC141, ENTPD1, KNL1, TTN, STAM, AC013652.1, NUSAP1
## CTNNAL1, MIR181A1HG, PBK, RRM2, ASPM, NCAPG, DIAPH3, SHCBP1, TOX, SPC25
## Negative: ANK3, MYBL1, THEMIS, STAT4, PLCB1, NR3C2, PITPNC1, ITGA4, UST, MCOLN2
## PDE4D, PRKCA, RBMS1, RASGRF2, PCSK5, ATP10A, TAFA1, SATB1-AS1, PRKN, PELI2
## PC_ 4
## Positive: RRM2, KIF18B, DIAPH3, SKA1, CDC6, RAD51AP1, FAM111B, STIL, E2F7, NCAPG
## PBK, TTK, ANLN, SHCBP1, SPC25, NUSAP1, DTL, CD109, POLQ, CDCA7L
## Negative: IKZF2, AC093865.1, TTN, ENTPD1, CCDC141, ST8SIA1, STAM, HPGD, TOX, LINC02694
## AF165147.1, FCRL3, CDHR3, RTKN2, DNAH8, GCNT4, HACD1, DUSP4, ST8SIA6, ATXN7L1
## PC_ 5
## Positive: APBA2, AL353660.1, ST8SIA1, FMN1, TRPS1, KCNQ5, TXK, TSHZ2, LINC01362, TMEM45B
## CARMIL1, ANKRD55, LEF1, LINC00402, FKBP5, IFNG-AS1, LINC01284, SLC9A9, SESN3, CERS6
## Negative: LINC00299, ADAM12, AL136456.1, FRY, MB21D2, SCART1, CCR6, MCF2L2, NIBAN1, DLEU1
## RUNX2, EEPD1, PDE4D, AGPAT4, HPGD, MTUS2, AFDN, NCAPG2, ANK1, PLCB1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.2350 -10.70 0.919 102.0000 1.02e+02 111.00
## 2 2 0.1370 -3.78 0.849 54.0000 5.38e+01 63.00
## 3 3 0.0483 -1.23 0.625 28.9000 2.86e+01 36.30
## 4 4 0.3030 -3.03 0.546 15.8000 1.54e+01 23.00
## 5 5 0.2990 -13.40 0.154 8.7800 8.47e+00 15.70
## 6 6 0.3320 -10.40 0.207 5.0000 4.77e+00 11.50
## 7 7 0.4030 -10.60 0.242 2.9200 2.69e+00 8.99
## 8 8 0.4330 -9.22 0.278 1.7500 1.54e+00 7.37
## 9 9 0.4490 -8.74 0.294 1.0900 8.93e-01 6.28
## 10 10 0.4570 -7.78 0.303 0.7030 5.28e-01 5.51
## 11 12 0.4470 -6.48 0.300 0.3310 1.90e-01 4.52
## 12 14 0.2550 -4.05 0.254 0.1860 6.65e-02 3.92
## 13 16 0.2530 -3.50 0.212 0.1230 2.41e-02 3.52
## 14 18 0.2270 -2.96 0.378 0.0925 9.13e-03 3.25
## 15 20 0.2360 -2.78 0.372 0.0760 3.67e-03 3.06
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5
## 136 17 13 11 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $blue
## [1] "INPP4B" "MAP3K1" "SERINC5" "RORA" "MGAT5" "ADAM19" "BCL2"
## [8] "PRKCA" "ANK3" "CDK6" "FRY" "MB21D2" "SOS1"
##
## $brown
## [1] "GNLY" "AOAH" "ZEB2" "C1orf21" "KLRD1" "OSBPL5"
## [7] "TGFBR3" "MVB12B" "PPP2R2B" "LINC02384" "PDGFD"
##
## $green
## [1] "IKZF2" "LINC02694" "AC093865.1" "CCDC141" "ENTPD1"
## [6] "TTN" "STAM" "AC013652.1" "HPGD" "ZC3H12C"
##
## $turquoise
## [1] "KNL1" "NUSAP1" "CTNNAL1" "PBK" "RRM2" "ASPM"
## [7] "NCAPG" "DIAPH3" "SHCBP1" "SPC25" "ARHGAP11A" "KIF18B"
## [13] "SKA1" "CDC6" "RAD51AP1" "FAM111B" "STIL" "E2F7"
## [19] "TTK" "ANLN" "DTL" "CD109" "POLQ" "CDCA7L"
## [25] "MKI67" "RACGAP1" "PCNA" "CDK1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "INPP4B" "MAP3K1" "SERINC5" "RORA" "MGAT5" "ADAM19" "BCL2"
## [8] "PRKCA" "ANK3" "CDK6" "FRY" "MB21D2" "SOS1"
##
## $brown
## [1] "GNLY" "AOAH" "ZEB2" "C1orf21" "KLRD1" "OSBPL5"
## [7] "TGFBR3" "MVB12B" "PPP2R2B" "LINC02384" "PDGFD"
##
## $green
## [1] "IKZF2" "LINC02694" "AC093865.1" "CCDC141" "ENTPD1"
## [6] "TTN" "STAM" "AC013652.1" "HPGD" "ZC3H12C"
##
## $turquoise
## [1] "KNL1" "NUSAP1" "CTNNAL1" "PBK" "RRM2" "ASPM"
## [7] "NCAPG" "DIAPH3" "SHCBP1" "SPC25" "ARHGAP11A" "KIF18B"
## [13] "SKA1" "CDC6" "RAD51AP1" "FAM111B" "STIL" "E2F7"
## [19] "TTK" "ANLN" "DTL" "CD109" "POLQ" "CDCA7L"
## [25] "MKI67" "RACGAP1" "PCNA" "CDK1"
##
## [1] "5009_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5999## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.7407e-15
## PC_ 1
## Positive: GNLY, ZEB2, SETBP1, AC243829.2, KLRK1, C1orf21, CCL5, RBFOX3, AOAH, KLRD1
## PRSS23, FAM49A, ADGRG5, ATP8B4, CLNK, MYO3B, PXDNL, SLCO4C1, LINC01505, SYNE1
## Negative: ARHGAP15, MBNL1, CAMK4, INPP4B, CDC14A, DPYD, PLCG2, MDFIC, MGAT5, RORA
## GPRIN3, RBMS1, HIVEP2, MAML2, SERINC5, ANTXR2, GNAQ, FBXL17, NR3C2, THEMIS
## PC_ 2
## Positive: ANK3, PRKCA, SERINC5, NR3C2, BCL2, NELL2, AC139720.1, LEF1, FAAH2, RASGRF2
## INPP4B, PCSK5, TSHZ2, MAN1C1, TXK, BACH2, SAMD12, CMTM8, RNF157, PELI2
## Negative: ZEB2, SAMD3, GNLY, TGFBR3, SETBP1, KLRD1, TOX, SYNE1, C12orf75, KLRK1
## PDGFD, AOAH, ARHGAP26, ATP8B4, FAM49A, MIR4435-2HG, RRM2, MYO3B, DIAPH3, PLEK
## PC_ 3
## Positive: ZEB2, GNLY, KLRD1, MCTP2, AOAH, KLRK1, PLEK, PDGFD, MYBL1, ATP8B4
## SLC4A4, PPP2R2B, FAM49A, SETBP1, A2M, KLRG1, MYO6, MYO3B, ADGRG5, KLRF1
## Negative: ASPM, DIAPH3, KIF18B, NCAPG, RRM2, BUB1B, KIF15, CDCA2, CDK1, ANLN
## E2F7, E2F8, MKI67, POLQ, TOP2A, GTSE1, KIF4A, KNL1, ESPL1, PCLAF
## PC_ 4
## Positive: LINC02694, STAM, FANK1, AC013652.1, TTN, CCDC141, SNED1, IKZF2, TOX, NIBAN1
## CTLA4, IL2RA, CDK14, IL7, AC093865.1, AL136456.1, CDHR3, MCF2L2, CYTOR, PLD1
## Negative: KIF18B, RRM2, CDCA2, KIF15, DIAPH3, KIFC1, ANK3, ANLN, E2F7, APBA2
## DEPDC1B, BUB1B, DLGAP5, FBXO5, POLQ, CDK1, CDCA8, E2F8, NR3C2, SPC25
## PC_ 5
## Positive: IKZF2, VAV3, AC093865.1, AL353660.1, TXK, SLC16A10, UBASH3B, CDK14, APBA2, SELL
## LINC00402, PLCL1, CCDC141, STAM, ATXN7L1, TTN, BACH1, GCNT4, TOX, CDHR3
## Negative: FRY, THEMIS, LINC00299, SLF1, SEPTIN11, ANXA1, AC079793.1, RBMS1, RORA, PTPN13
## MSC-AS1, PLD1, RUNX2, ITGB1, KIAA0825, TGFBR3, RBPJ, GTDC1, LINC00511, CDK6
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00340 -1.760 0.7810 108.0000 1.08e+02 115.00
## 2 2 0.00704 1.040 0.7050 57.1000 5.65e+01 64.90
## 3 3 0.11000 -2.360 0.5850 30.5000 3.01e+01 38.70
## 4 4 0.36100 -2.870 0.5190 16.6000 1.61e+01 24.40
## 5 5 0.50500 -2.620 0.4620 9.2600 8.74e+00 16.30
## 6 6 0.76500 -2.570 0.6980 5.2900 4.80e+00 11.60
## 7 7 0.81000 -2.350 0.7930 3.1100 2.65e+00 8.68
## 8 8 0.77500 -2.060 0.8150 1.8900 1.49e+00 6.77
## 9 9 0.72000 -1.860 0.7810 1.2000 8.48e-01 5.46
## 10 10 0.20300 -3.310 -0.0249 0.7860 4.89e-01 4.50
## 11 12 0.73200 -1.360 0.7990 0.3820 1.71e-01 3.21
## 12 14 0.78600 -1.140 0.8380 0.2140 5.90e-02 2.45
## 13 16 0.87600 -1.090 0.8890 0.1330 2.06e-02 1.93
## 14 18 0.88200 -1.030 0.8580 0.0887 7.35e-03 1.55
## 15 20 0.91700 -0.998 0.8970 0.0623 2.78e-03 1.27
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7
## 105 30 18 13 12 11 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $turquoise
## [1] "GNLY" "ZEB2" "SETBP1" "AC243829.2" "KLRK1"
## [6] "C1orf21" "CCL5" "RBFOX3" "AOAH" "KLRD1"
## [11] "PRSS23" "FAM49A" "ADGRG5" "ATP8B4" "MYO3B"
## [16] "SYNE1" "RIN3" "SAMD3" "TGFBR3" "C12orf75"
## [21] "PDGFD" "ARHGAP26" "PLEK" "MYBL1" "PPP2R2B"
## [26] "A2M" "KLRG1" "DTHD1" "SYTL2" "AGAP1"
##
## $brown
## [1] "ARHGAP15" "MBNL1" "INPP4B" "DPYD" "PLCG2"
## [6] "MDFIC" "RORA" "RBMS1" "MAML2" "SERINC5"
## [11] "ANTXR2" "NR3C2" "THEMIS" "SSBP2" "ANK3"
## [16] "AC079793.1" "PRKCA" "BCL2" "NELL2" "AC139720.1"
## [21] "LEF1" "RASGRF2" "MAN1C1" "TXK" "BACH2"
## [26] "SAMD12" "KCNQ1" "AC233976.1" "AL353660.1" "SELL"
## [31] "LINC00402" "GCNT4" "PTPN13" "CDK6" "ERN1"
##
## $blue
## [1] "RRM2" "DIAPH3" "KIFC1" "POLQ" "ASPM" "KIF18B" "NCAPG"
## [8] "BUB1B" "KIF15" "CDCA2" "CDK1" "ANLN" "E2F7" "E2F8"
## [15] "MKI67" "TOP2A" "GTSE1" "KIF4A" "KNL1" "ESPL1" "PCLAF"
## [22] "DLGAP5" "CDCA8" "SHCBP1" "STMN1" "DEPDC1B" "FBXO5" "SPC25"
## [29] "CDC25C" "PLEKHA5"
##
## $black
## [1] "STAM" "FANK1" "TTN" "CCDC141" "CTLA4"
## [6] "IL2RA" "MIR181A1HG" "SLC16A10" "TSHR" "RTKN2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "3/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "GNLY" "ZEB2" "SETBP1" "AC243829.2" "KLRK1"
## [6] "C1orf21" "CCL5" "RBFOX3" "AOAH" "KLRD1"
## [11] "PRSS23" "FAM49A" "ADGRG5" "ATP8B4" "MYO3B"
## [16] "SYNE1" "RIN3" "SAMD3" "TGFBR3" "C12orf75"
## [21] "PDGFD" "ARHGAP26" "PLEK" "MYBL1" "PPP2R2B"
## [26] "A2M" "KLRG1" "DTHD1" "SYTL2" "AGAP1"
##
## $brown
## [1] "ARHGAP15" "MBNL1" "INPP4B" "DPYD" "PLCG2"
## [6] "MDFIC" "RORA" "RBMS1" "MAML2" "SERINC5"
## [11] "ANTXR2" "NR3C2" "THEMIS" "SSBP2" "ANK3"
## [16] "AC079793.1" "PRKCA" "BCL2" "NELL2" "AC139720.1"
## [21] "LEF1" "RASGRF2" "MAN1C1" "TXK" "BACH2"
## [26] "SAMD12" "KCNQ1" "AC233976.1" "AL353660.1" "SELL"
## [31] "LINC00402" "GCNT4" "PTPN13" "CDK6" "ERN1"
##
## $blue
## [1] "RRM2" "DIAPH3" "KIFC1" "POLQ" "ASPM" "KIF18B" "NCAPG"
## [8] "BUB1B" "KIF15" "CDCA2" "CDK1" "ANLN" "E2F7" "E2F8"
## [15] "MKI67" "TOP2A" "GTSE1" "KIF4A" "KNL1" "ESPL1" "PCLAF"
## [22] "DLGAP5" "CDCA8" "SHCBP1" "STMN1" "DEPDC1B" "FBXO5" "SPC25"
## [29] "CDC25C" "PLEKHA5"
##
## $black
## [1] "STAM" "FANK1" "TTN" "CCDC141" "CTLA4"
## [6] "IL2RA" "MIR181A1HG" "SLC16A10" "TSHR" "RTKN2"
##
## [1] "5009_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.2262## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32308## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, GPRIN3, CD28, INPP4B, DPYD, ELMO1, SERINC5, USP3, MGAT5, EML4
## ZBTB20, FAAH2, SMCHD1, STT3B, TTC39C, SFXN1, PDE3B, CAMK4, PDE7A, ADK
## Negative: ZEB2, TRBV23-1, RHBDF2, RPS19, RPS27A, GNLY, ATP8B4, SHTN1, C1orf21, C5orf17
## RPL41, KLRD1, TFAP2A-AS1, FAM49A, OSBPL5, GSN, ZNF347, LINC02664, MVB12B, LINC00667
## PC_ 2
## Positive: ANK3, LEF1, BCL2, RCAN3, FAAH2, TSHZ2, PRKCA, NELL2, CMTM8, PVT1
## ADAM19, SERINC5, PELI2, GNAQ, TTC39C, PAG1, AC139720.1, RASGRF2, TMEM123, AC233976.1
## Negative: ZEB2, ARHGAP26, CEP78, AOAH, GNLY, CMIP, SAMD3, C1orf21, TGFBR3, PPP2R2B
## SETBP1, MYO3B, NCALD, PPM1L, RABGAP1L, OSBPL5, NAA50, AGAP1, KLRG1, PDGFD
## PC_ 3
## Positive: RAPGEF2, ARHGAP26, SAMD3, NCALD, SSBP3, ARAP2, PTPN12, ZBTB20, PPP2R2B, ANKRD28
## NIBAN1, NSMAF, RAP1GDS1, ZEB2, KLRG1, ZNF407, TGFBR3, MYO6, SGMS1, PLEKHA5
## Negative: BAD, KIF11, BUB1B, MAP1S, CCNA2, CCNE2, CDCA8, PLXDC1, AGA, POC1A
## MLC1, KNL1, IQCH, GDAP1, ZNF16, KPNA2, GPSM2, CENPO, MBOAT2, REXO5
## PC_ 4
## Positive: LINC01588, MRPL50, NR3C2, TFDP2, EFCAB6, AC139720.1, DNAJC6, SINHCAF, AL353660.1, PITPNC1
## FBXO38, NEXMIF, RNF19B, ZC4H2, SPECC1L, AC011447.3, OCRL, MAP2K6, TRABD2A, PRKN
## Negative: ADAM12, C15orf39, LRP12, AC019117.1, PLD1, RORA-AS1, SNED1, LINC02694, AC104365.1, ELOVL4
## AC013652.1, LINC00598, MCF2L2, AL589990.1, ATP13A4, C16orf95, RPS17, TMSB10, ENTPD5, FRY
## PC_ 5
## Positive: TMSB10, AP001011.1, RPL28, ACTG1, AC104365.1, RPS17, GLIPR1, S100A6, AC079793.1, LTB
## RPLP2, FOSB, RPL34, SH3BGRL3, ATP6AP1, FAU, JUN, EEF1A1, PRTFDC1, TEX14
## Negative: CD80, AC019117.1, NLN, CZIB, TMEM178B, C16orf95, ELOVL4, AC007220.1, MICU3, GSKIP
## POLE2, AL096803.2, ANK1, CENPQ, EMC1, AL138720.1, PRKAR1B, CCDC200, CDK6, STPG1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.000157 0.203 0.6280 111.0000 112.0000 118.000
## 2 2 0.003660 0.529 0.5710 58.8000 59.0000 66.800
## 3 3 0.012500 -0.729 0.6090 31.7000 31.7000 39.300
## 4 4 0.142000 -2.210 0.8030 17.4000 17.4000 24.100
## 5 5 0.234000 -2.440 0.7620 9.7800 9.7600 15.400
## 6 6 0.451000 -2.800 0.8170 5.6100 5.6100 10.300
## 7 7 0.240000 -6.190 0.1780 3.3000 3.3100 7.170
## 8 8 0.267000 -5.510 0.2020 1.9900 1.9700 5.170
## 9 9 0.187000 -4.080 -0.0437 1.2300 1.2000 3.860
## 10 10 0.756000 -2.450 0.7720 0.7780 0.7440 2.950
## 11 12 0.182000 -3.050 -0.0150 0.3370 0.3010 1.850
## 12 14 0.145000 -3.220 -0.0396 0.1610 0.1220 1.240
## 13 16 0.358000 -4.670 0.2390 0.0847 0.0526 0.868
## 14 18 0.285000 -4.340 0.0832 0.0487 0.0240 0.668
## 15 20 0.244000 -3.610 0.0575 0.0303 0.0114 0.559
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3
## 173 20 12 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $brown
## [1] "RPS19" "RPS27A" "RPL41" "RPS17" "TMSB10" "FAU" "RPL28" "LTB"
## [9] "RPLP2" "RPL34"
##
## $turquoise
## [1] "MAP1S" "BAD" "KIF11" "BUB1B" "CCNA2" "CCNE2" "CDCA8" "PLXDC1"
## [9] "MLC1" "KNL1" "IQCH" "GDAP1" "KPNA2" "CENPO" "REXO5" "POLD1"
## [17] "ORC1" "ZNF850" "NDC80" "FBXO5"
##
## $blue
## [1] "AC019117.1" "ELOVL4" "LINC00598" "ATP13A4" "GSKIP"
## [6] "CZIB" "AC007220.1" "AL096803.2" "CENPQ" "EMC1"
## [11] "CCDC200" "STPG1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "RPS19" "RPS27A" "RPL41" "RPS17" "TMSB10" "FAU" "RPL28" "LTB"
## [9] "RPLP2" "RPL34"
##
## $turquoise
## [1] "MAP1S" "BAD" "KIF11" "BUB1B" "CCNA2" "CCNE2" "CDCA8" "PLXDC1"
## [9] "MLC1" "KNL1" "IQCH" "GDAP1" "KPNA2" "CENPO" "REXO5" "POLD1"
## [17] "ORC1" "ZNF850" "NDC80" "FBXO5"
##
## $blue
## [1] "AC019117.1" "ELOVL4" "LINC00598" "ATP13A4" "GSKIP"
## [6] "CZIB" "AC007220.1" "AL096803.2" "CENPQ" "EMC1"
## [11] "CCDC200" "STPG1"
##
## [1] "5003_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3748## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32366## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.2183e-31## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, RORA, LRRC8C, MBNL1, DPYD, ZBTB20, CELF2, ANKRD44, LINC01619, ELMO1
## RUNX1, PARP8, SP3, KLF12, MCTP2, TCF12, TGFBR3, RBMS1, INPP4B, NIBAN1
## Negative: RPS18, RPL13, RPLP1, RPL39, RPS27, RPL41, RPS28, RPS12, RPL11, RPL34
## RPL32, RPL9, RPL23, RPS21, RPL8, RPL23A, RPL37A, RPL35, RPS2, RPL10
## PC_ 2
## Positive: C1orf21, ZEB2, PDGFD, GNLY, MAP3K8, PPP2R2B, AGPAT4, SGCD, PROK2, VAV3
## SYNE1, LINC02384, ETHE1, MSC-AS1, ARHGEF12, RGS3, PLXND1, SLC4A8, NDUFB6, TMCC3
## Negative: RPL13, ANK3, RPL34, RPS2, INPP4B, RPL39, RPS12, RPL21, CDC14A, RPL41
## RPL23, RPL30, RPLP1, RPS18, RPS27, RPL37A, RPS28, RPL11, RPL35, SERINC5
## PC_ 3
## Positive: CCDC141, TSHR, IKZF2, FOXP3, AC093865.1, LINC02694, LINC00426, TOX, STAM, RTKN2
## TTN, LYRM1, SLC16A10, CDHR3, MIR181A1HG, CTLA4, ST8SIA4, FANK1, ENTPD1, ATXN7L1
## Negative: PLCB1, PDGFD, C1orf21, GNLY, MYBL1, ZEB2, MCTP2, PTPRM, LINC02384, ANK3
## CASC8, PROK2, PAFAH2, THEMIS, PELI2, NDUFB6, ARHGAP26, ATP10A, SGCD, SYTL2
## PC_ 4
## Positive: RPS28, RPL37A, RPL41, RPS2, RPL34, RPL11, RPL39, RPS21, RPLP1, RPS27
## RPS18, RPL10, RPL23, RPS12, RPS15, RPL30, RPL9, RPL13, RPL18, RPL23A
## Negative: TMEM131L, CCND3, CERS6, FHIT, PRKCA, ITPKB, TSHZ2, KCNQ1, SGK3, ASCC1
## ATP11C, SNAI3-AS1, ZBTB26, CMTM8, AL589693.1, Z94721.1, ZNF710, AC040934.1, PRKAG2, UNC50
## PC_ 5
## Positive: TTLL7, FAM214B, C5orf30, GCA, FRY, MAML3, BHLHE40-AS1, KIAA0825, TMEM200A, ZNF418
## UFL1-AS1, SMIM12, AC008014.1, COL24A1, DSCAML1, IATPR, PKP4, ZNF81, MMRN1, ANKRD28
## Negative: IER3IP1, Z98884.1, ADAL, AC084125.2, CERS6, TRMT11, GCNT2, RGL1, YAE1, METTL8
## SNX30, ZNF627, CLN6, RNLS, AC007262.2, GRPEL2, MRC2, MCM8, POLD3, EXT1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.03100 6.090 0.85600 118.0000 118.0000 125.000
## 2 2 0.05240 4.110 0.75200 61.7000 61.3000 68.600
## 3 3 0.04370 2.330 0.85200 32.6000 32.4000 38.100
## 4 4 0.00667 0.666 0.88600 17.5000 17.4000 21.900
## 5 5 0.03550 -1.170 0.90200 9.5600 9.4700 13.000
## 6 6 0.07580 -1.320 0.79500 5.3200 5.2300 7.960
## 7 7 0.24200 -1.680 0.87500 3.0100 2.9200 5.030
## 8 8 0.52100 -2.150 0.88500 1.7500 1.6700 3.490
## 9 9 0.65500 -2.230 0.87600 1.0400 0.9500 2.510
## 10 10 0.81000 -2.290 0.90000 0.6320 0.5500 1.840
## 11 12 0.91300 -1.960 0.93400 0.2530 0.1950 1.040
## 12 14 0.92900 -1.830 0.91100 0.1130 0.0702 0.656
## 13 16 0.22600 -2.850 0.00466 0.0551 0.0264 0.501
## 14 18 0.28100 -3.660 0.08700 0.0293 0.0109 0.397
## 15 20 0.29100 -3.910 0.08790 0.0167 0.0045 0.323
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3
## 179 26 15 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $turquoise
## [1] "RPS18" "RPL13" "RPLP1" "RPL39" "RPS27" "RPL41" "RPS28" "RPS12"
## [9] "RPL11" "RPL34" "RPL32" "RPL9" "RPL23" "RPS21" "RPL8" "RPL23A"
## [17] "RPL37A" "RPL35" "RPS2" "RPL10" "RPL18" "RPL30" "RPL12" "RPL21"
## [25] "RPS15" "RPS3"
##
## $brown
## [1] "C1orf21" "ZEB2" "PDGFD" "GNLY" "PPP2R2B" "AGPAT4"
## [7] "SYNE1" "LINC02384" "TMCC3" "PLCB1"
##
## $blue
## [1] "TTLL7" "GCA" "TMEM200A" "SMIM12" "COL24A1" "DSCAML1"
## [7] "MMRN1" "GPR82" "MYO16" "RRAGD" "DPF3" "TMEM67"
## [13] "LY86" "ADAM23" "DCBLD1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "RPS18" "RPL13" "RPLP1" "RPL39" "RPS27" "RPL41" "RPS28" "RPS12"
## [9] "RPL11" "RPL34" "RPL32" "RPL9" "RPL23" "RPS21" "RPL8" "RPL23A"
## [17] "RPL37A" "RPL35" "RPS2" "RPL10" "RPL18" "RPL30" "RPL12" "RPL21"
## [25] "RPS15" "RPS3"
##
## $brown
## [1] "C1orf21" "ZEB2" "PDGFD" "GNLY" "PPP2R2B" "AGPAT4"
## [7] "SYNE1" "LINC02384" "TMCC3" "PLCB1"
##
## $blue
## [1] "TTLL7" "GCA" "TMEM200A" "SMIM12" "COL24A1" "DSCAML1"
## [7] "MMRN1" "GPR82" "MYO16" "RRAGD" "DPF3" "TMEM67"
## [13] "LY86" "ADAM23" "DCBLD1"
##
## [1] "5003_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3214## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49966## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.8442e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: RBMS1, ARHGAP15, PIP4K2A, PARP8, CBLB, MBNL1, SSH2, STK39, PPP3CA, CELF2
## ZBTB20, PHACTR2, CATSPERB, PAG1, GRAMD2B, FBXO11, MAML2, UMAD1, ANTXR2, SLC16A7
## Negative: TMSB10, HLA-C, TMSB4X, JUN, FOS, GAPDH, MALAT1, AC022217.3, UQCRB, CCDC141
## IKZF2, BTF3, IL5RA, TTN, TPI1, LGALS1, S100A4, LINC02422, ARL4A, CSKMT
## PC_ 2
## Positive: PRKCA, ANK3, INPP4B, CDC14A, DOCK10, MDFIC, DENND5A, NELL2, ARHGAP15, AC139720.1
## MGAT5, BCL2, TSHZ2, HIVEP2, RBMS1, PCSK5, RASGRF2, PITPNC1, KCNQ1, APBA2
## Negative: TOX, ZEB2, PDGFD, C1orf21, TRGC2, AC093865.1, VAV3, NDUFAF4, IKZF2, PEX5
## EPB41L4A, PGPEP1, ADGRG1, HLA-DRB1, KLRK1, DMXL2, CMKLR1, ATP6V0A1, LINC02694, PPP2R2B
## PC_ 3
## Positive: LINC02694, STAM, ENTPD1, IKZF2, AC013652.1, AC093865.1, RTKN2, PLCL1, MAP3K1, F5
## HMCN1, S100A4, IL2RA, TTN, CDHR3, DLEU7, SNED1, PALM2-AKAP2, TAFA2, GPA33
## Negative: PDGFD, C1orf21, ZEB2, PITPNC1, TRGC2, PLCB1, THEMIS, PTPRM, EPB41L4A, KLRK1
## PTGDR, GNLY, SAMD3, MCOLN2, DTHD1, AGAP1, AOAH, IL18RAP, GAS7, MYO6
## PC_ 4
## Positive: SH3RF3, EDAR, RHCE, SGO2, ANKRD24, FBXL14, PACRG, NEBL, AC092535.4, AGPAT5
## AC119403.1, EEF1AKMT1, SNX18, ACER1, TULP4, ALDH8A1, PTPA, GCNT2, AC079447.1, WNT5B
## Negative: FRY, SLC13A3, ZNF570, RUNX2, MSC-AS1, EEPD1, MB21D2, ABCB1, AUTS2, LINC02694
## DTHD1, PKIA, LMNA, CPNE8, HTRA4, SEPTIN11, CMC1, PTPN13, HDGFL3, CIITA
## PC_ 5
## Positive: BAALC-AS1, DRD3, ZNF570, HDX, DMPK, NEK10, TMED3, TPTE2, AC024028.1, SLC13A3
## LINC01727, NECTIN3, HEATR9, WDR63, RBBP8, ZDHHC7, AC009315.1, EPB41L2, DNMBP, DTHD1
## Negative: HLA-C, TNFAIP3, PLCB1, EMILIN2, LMNA, IFNG-AS1, FOS, ERLIN1, COX8A, WAKMAR2
## SEMA4A, HBS1L, IL32, JAM3, AP4M1, BTG3, PACSIN1, IL12RB2, SPIRE1, C4orf33
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.23100 16.800 0.8030 92.10000 92.40000 96.5000
## 2 2 0.24600 8.710 0.6820 48.00000 48.40000 52.5000
## 3 3 0.41200 7.270 0.8490 25.40000 25.60000 28.8000
## 4 4 0.38700 5.070 0.8160 13.60000 13.70000 16.2000
## 5 5 0.17900 12.100 0.0547 7.38000 7.41000 9.4700
## 6 6 0.03290 0.964 0.4970 4.07000 4.04000 5.7200
## 7 7 0.00357 -0.240 0.7620 2.29000 2.26000 3.5600
## 8 8 0.02900 -0.561 0.8170 1.31000 1.26000 2.2900
## 9 9 0.09020 -0.843 0.8590 0.76500 0.72300 1.5200
## 10 10 0.14900 -0.937 0.9180 0.45600 0.41900 1.0400
## 11 12 0.38300 -1.250 0.8370 0.17300 0.14600 0.5280
## 12 14 0.25900 -3.970 0.1540 0.07180 0.05170 0.2920
## 13 16 0.92700 -1.780 0.9310 0.03260 0.01970 0.1720
## 14 18 0.87800 -1.660 0.8470 0.01610 0.00765 0.1060
## 15 20 0.09780 -1.780 -0.0660 0.00853 0.00317 0.0669
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7
## 83 22 19 12 12 11 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.## $yellow
## [1] "RBMS1" "ARHGAP15" "PIP4K2A" "PARP8" "CBLB"
## [6] "MBNL1" "PPP3CA" "CELF2" "ZBTB20" "MAML2"
## [11] "UMAD1" "ANTXR2" "SLC4A7" "STAT4" "PRKCA"
## [16] "ANK3" "INPP4B" "CDC14A" "DOCK10" "MDFIC"
## [21] "NELL2" "AC139720.1" "MGAT5" "BCL2" "HIVEP2"
## [26] "PCSK5" "RASGRF2" "PITPNC1" "KCNQ1" "PRKN"
## [31] "MAN1C1" "SBF2" "THEMIS" "MB21D2"
##
## $green
## [1] "TMSB10" "HLA-C" "TMSB4X" "GAPDH" "UQCRB"
## [6] "BTF3" "LGALS1" "S100A4" "AC087286.2" "IL32"
## [11] "HLA-DRB1"
##
## $blue
## [1] "CCDC141" "IKZF2" "TTN" "TOX" "AC093865.1"
## [6] "VAV3" "LINC02694" "AC013652.1" "STAM" "RTKN2"
## [11] "PLCL1" "IL2RA" "CDHR3" "DLEU7" "SNED1"
## [16] "PALM2-AKAP2" "TAFA2" "AL136456.1" "MSC-AS1"
##
## $red
## [1] "ZEB2" "KLRK1" "ACSL1" "MCOLN2" "AOAH" "ALDH18A1"
## [7] "DMPK" "TRGC1" "SLC4A4" "SLC13A3" "CIITA"
##
## $turquoise
## [1] "SH3RF3" "EDAR" "RHCE" "SGO2" "ANKRD24"
## [6] "FBXL14" "PACRG" "NEBL" "AC092535.4" "AGPAT5"
## [11] "AC119403.1" "EEF1AKMT1" "SNX18" "ACER1" "ALDH8A1"
## [16] "PTPA" "GCNT2" "AC079447.1" "WNT5B" "SDHD"
## [21] "AL353660.1" "EPN2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "RBMS1" "ARHGAP15" "PIP4K2A" "PARP8" "CBLB"
## [6] "MBNL1" "PPP3CA" "CELF2" "ZBTB20" "MAML2"
## [11] "UMAD1" "ANTXR2" "SLC4A7" "STAT4" "PRKCA"
## [16] "ANK3" "INPP4B" "CDC14A" "DOCK10" "MDFIC"
## [21] "NELL2" "AC139720.1" "MGAT5" "BCL2" "HIVEP2"
## [26] "PCSK5" "RASGRF2" "PITPNC1" "KCNQ1" "PRKN"
## [31] "MAN1C1" "SBF2" "THEMIS" "MB21D2"
##
## $green
## [1] "TMSB10" "HLA-C" "TMSB4X" "GAPDH" "UQCRB"
## [6] "BTF3" "LGALS1" "S100A4" "AC087286.2" "IL32"
## [11] "HLA-DRB1"
##
## $blue
## [1] "CCDC141" "IKZF2" "TTN" "TOX" "AC093865.1"
## [6] "VAV3" "LINC02694" "AC013652.1" "STAM" "RTKN2"
## [11] "PLCL1" "IL2RA" "CDHR3" "DLEU7" "SNED1"
## [16] "PALM2-AKAP2" "TAFA2" "AL136456.1" "MSC-AS1"
##
## $red
## [1] "ZEB2" "KLRK1" "ACSL1" "MCOLN2" "AOAH" "ALDH18A1"
## [7] "DMPK" "TRGC1" "SLC4A4" "SLC13A3" "CIITA"
##
## $turquoise
## [1] "SH3RF3" "EDAR" "RHCE" "SGO2" "ANKRD24"
## [6] "FBXL14" "PACRG" "NEBL" "AC092535.4" "AGPAT5"
## [11] "AC119403.1" "EEF1AKMT1" "SNX18" "ACER1" "ALDH8A1"
## [16] "PTPA" "GCNT2" "AC079447.1" "WNT5B" "SDHD"
## [21] "AL353660.1" "EPN2"
##
## [1] "5016_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.538## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50061## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.8257e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: CAMK4, LEF1, PRKCA, SERINC5, INPP4B, ANK3, TSHZ2, HIVEP2, MAML2, CDC14A
## MAP3K1, PAG1, CSGALNACT1, CD28, GNAQ, TTC39C, PDE3B, MGAT5, ZEB1, PLCL1
## Negative: AOAH, ZEB2, AC243829.2, C1orf21, TGFBR3, GNLY, PPP2R2B, SAMD3, KLRD1, ARHGAP26
## SETBP1, VAV3, SGCD, DTHD1, LINC02384, OSBPL5, KLRG1, MCTP2, JAZF1, AL392086.3
## PC_ 2
## Positive: RPLP1, RPLP2, RPL13, RPL28, RPL41, RPS2, RPL3, RPL13A, RPL19, RPL10A
## FAU, RPL30, FOS, EEF1A1, JUN, FOSB, DNAJA1, JUNB, AC022217.3, TUBA1A
## Negative: CHST11, RORA, KLF12, PPP1R16B, GPRIN3, ARHGAP15, MAP3K5, CD247, LINC00944, RUNX1
## GALNT1, NIBAN1, JAZF1, SAMD3, OSBPL3, PPP2R2B, PAM, PRR5L, HIVEP3, SLC9A9
## PC_ 3
## Positive: UBASH3B, MAML3, SLC16A10, AC106795.3, CD28, SH3RF3, LINC01550, LINC01135, NAV1, AC139720.1
## FRMD3, PRKCA, GCNT4, AL589693.1, IL2RA, APOLD1, SERTAD2, LINC01483, ZNRF1, LYRM9
## Negative: JUN, FOS, FOSB, RPL3, DNAJA1, JUNB, RPS2, RPL13A, DDX3Y, SLC38A2
## TEX14, RPL10A, FAU, RPL41, AL606489.1, RPLP2, IFRD1, IER5, AC022217.3, RPL28
## PC_ 4
## Positive: LINC02694, AC013652.1, KIAA0825, MSC-AS1, NIBAN1, HPGD, BCL2L11, DLEU2, CHDH, PARP2
## HHAT, RTKN2, GNB4, DUSP10, CENPP, OSBPL1A, SNED1, E2F3, PAG1, MCF2L2
## Negative: TXK, IGF1R, CERS6, PCSK5, OSBPL5, ARHGAP32, SAMD12, PRKN, EPB41L4A, NCAM1
## CMTM8, PELI2, AL392086.3, ZNF146, AC233976.1, KANK1, SATB1-AS1, GNLY, KLRF1, KLRC3
## PC_ 5
## Positive: THEMIS, ITGA4, IFNG-AS1, CMC1, AL590006.1, TRPS1, PRKCB, LINC01934, LINC02725, NELL2
## ST8SIA1, SBF2, WHRN, E2F3, TASP1, CBLB, AC243829.1, AC006369.1, MYOM1, GZMK
## Negative: CTBP2, FRY, LINC00511, LINC02694, CERNA1, PLD1, ZBTB16, SNED1, MIR646HG, AC013652.1
## HPGD, AC005237.1, CSGALNACT1, EGLN3, SEMA5A, RTKN2, AC122685.1, BNC2, TXNDC5, ADCK1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 1.55e-05 -0.155 0.8790 84.3000 84.40000 88.200
## 2 2 2.04e-01 8.970 0.8650 43.8000 43.50000 47.700
## 3 3 1.01e-01 2.930 0.7480 23.3000 23.20000 27.000
## 4 4 3.36e-02 0.824 0.8640 12.7000 12.50000 16.200
## 5 5 1.22e-01 -1.190 0.8650 7.0900 6.86000 10.800
## 6 6 4.95e-01 -1.970 0.8040 4.0700 3.88000 7.630
## 7 7 7.36e-01 -2.000 0.8210 2.4100 2.20000 5.570
## 8 8 8.93e-01 -2.010 0.9240 1.4700 1.27000 4.170
## 9 9 9.21e-01 -1.830 0.9090 0.9290 0.73700 3.190
## 10 10 9.47e-01 -1.700 0.9320 0.6030 0.43400 2.480
## 11 12 8.04e-01 -1.520 0.7610 0.2780 0.15800 1.540
## 12 14 8.56e-01 -1.370 0.8260 0.1410 0.05790 0.991
## 13 16 8.22e-01 -1.240 0.8140 0.0778 0.02210 0.668
## 14 18 9.87e-02 -1.540 -0.0639 0.0455 0.00864 0.465
## 15 20 1.60e-01 -1.860 -0.0738 0.0279 0.00358 0.327
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5
## 93 18 15 15 13 13
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $turquoise
## [1] "CAMK4" "LEF1" "PRKCA" "SERINC5" "INPP4B"
## [6] "ANK3" "TSHZ2" "HIVEP2" "MAML2" "CDC14A"
## [11] "MAP3K1" "PAG1" "CSGALNACT1" "GNAQ" "TTC39C"
## [16] "PDE3B" "MGAT5" "ZEB1" "PLCL1" "RASGRF2"
## [21] "TMEM123" "FAAH2" "EPHA4" "ARHGAP15" "ZBTB20"
## [26] "AC139720.1" "PCSK5" "SAMD12" "CMTM8" "AC233976.1"
## [31] "SATB1-AS1"
##
## $blue
## [1] "AOAH" "ZEB2" "AC243829.2" "C1orf21" "TGFBR3"
## [6] "PPP2R2B" "SAMD3" "ARHGAP26" "VAV3" "DTHD1"
## [11] "LINC02384" "AL392086.3" "CMIP" "HIVEP3" "SYTL2"
##
## $brown
## [1] "RPLP1" "RPLP2" "RPL13" "RPL28" "RPL41"
## [6] "RPS2" "RPL3" "RPL13A" "RPL19" "RPL10A"
## [11] "FAU" "RPL30" "FOS" "EEF1A1" "JUN"
## [16] "FOSB" "DNAJA1" "JUNB" "AC022217.3" "TUBA1A"
## [21] "IER2" "AL606489.1" "IER5" "DDX3Y" "SLC38A2"
## [26] "TEX14" "IFRD1" "ID2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "CAMK4" "LEF1" "PRKCA" "SERINC5" "INPP4B"
## [6] "ANK3" "TSHZ2" "HIVEP2" "MAML2" "CDC14A"
## [11] "MAP3K1" "PAG1" "CSGALNACT1" "GNAQ" "TTC39C"
## [16] "PDE3B" "MGAT5" "ZEB1" "PLCL1" "RASGRF2"
## [21] "TMEM123" "FAAH2" "EPHA4" "ARHGAP15" "ZBTB20"
## [26] "AC139720.1" "PCSK5" "SAMD12" "CMTM8" "AC233976.1"
## [31] "SATB1-AS1"
##
## $blue
## [1] "AOAH" "ZEB2" "AC243829.2" "C1orf21" "TGFBR3"
## [6] "PPP2R2B" "SAMD3" "ARHGAP26" "VAV3" "DTHD1"
## [11] "LINC02384" "AL392086.3" "CMIP" "HIVEP3" "SYTL2"
##
## $brown
## [1] "RPLP1" "RPLP2" "RPL13" "RPL28" "RPL41"
## [6] "RPS2" "RPL3" "RPL13A" "RPL19" "RPL10A"
## [11] "FAU" "RPL30" "FOS" "EEF1A1" "JUN"
## [16] "FOSB" "DNAJA1" "JUNB" "AC022217.3" "TUBA1A"
## [21] "IER2" "AL606489.1" "IER5" "DDX3Y" "SLC38A2"
## [26] "TEX14" "IFRD1" "ID2"
##
## [1] "5035_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7698## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.5018## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.156e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: RPL13, RPLP2, INPP4B, RPL41, RPS12, RPS2, RPL3, RPL13A, JUN, TSHZ2
## LEF1, CAMK4, FOSB, FOS, JUNB, SERINC5, PRKCA, FHIT, ANK3, IER2
## Negative: ZEB2, C1orf21, AOAH, TGFBR3, GNLY, PPP2R2B, OSBPL5, SYNE1, AC243829.2, NCALD
## KLRC3, SETBP1, KLRD1, SGCD, LYN, KLRK1, ADGRG5, VAV3, KLRF1, LINC02384
## PC_ 2
## Positive: C1orf21, RPL13A, ZEB2, GNLY, RPLP2, RPS12, CTBP2, KLRC3, SETBP1, RPL13
## KLRK1, RPL41, OSBPL5, AOAH, RPL3, LYN, AC243829.2, PRSS23, EPB41L4A, NCAM1
## Negative: INPP4B, PAG1, ARHGAP15, CAMK4, CDC14A, SERINC5, ANK3, MGAT5, THEMIS, RORA
## HIVEP2, ZBTB20, PRKCA, NR3C2, MDFIC, TNFAIP8, FMN1, PATJ, FOXP1, CD44
## PC_ 3
## Positive: PVT1, F5, XYLT1, ZMIZ1, ADAM19, AP002383.2, LINC02694, ST8SIA1, AL136456.1, AC006369.1
## TOX, MCC, PTPRJ, SLC16A1-AS1, MIB1, Z94721.1, PTPN13, MBOAT1, FBXL18, AC027097.2
## Negative: JUN, FOSB, JUNB, IFRD1, FOS, RPL41, DNAJA1, DDX3Y, IER2, NAMPT
## RPS12, RPL13A, DUSP1, RPS2, RPL13, RPLP2, EGR1, EIF4A3, SLC2A3, RPL3
## PC_ 4
## Positive: LINC02694, TOX, TTN, ENTPD1, ST8SIA1, IKZF2, LINC01362, SEMA5A, GLCCI1, ATXN1
## AC013652.1, RTKN2, CDRT4, LINC02725, ST8SIA6, PAM, LINC00426, NIBAN1, CYTOR, S100Z
## Negative: PTPN13, PLCB1, ADAM12, PCSK5, CCR6, PDE4D, BCL2, SASH1, ANK1, GREM2
## CR1, AFDN, BACH2, PLXNA4, MB21D2, ABCB1, IGF1R, COL5A3, RBMS1, PELI2
## PC_ 5
## Positive: FRY, LINC02694, PTPN13, ADAM12, PDE4D, COL5A3, AL136456.1, C21orf91-OT1, AUTS2, NIBAN1
## LRP12, LINC00299, NEDD4L, NAMPT, STAM, AC013652.1, CCR6, MCF2L2, MSC-AS1, SEMA5A
## Negative: IGF1R, AK5, EPHA1-AS1, SORCS3, NELL2, MAML2, LEF1, CERS6, ACTN1, FHIT
## UBE2E2, PTPDC1, BCL9, AC233976.1, TSHZ2, SESN3, PRKN, EDAR, MTMR8, MAN1C1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.1180 -13.60 0.82900 77.2000 77.20000 80.500
## 2 2 0.0197 -2.59 0.96500 40.2000 40.30000 43.700
## 3 3 0.1540 -4.41 0.95700 21.3000 21.40000 24.900
## 4 4 0.4870 -5.63 0.87200 11.6000 11.70000 15.600
## 5 5 0.6720 -4.72 0.84600 6.4100 6.38000 10.300
## 6 6 0.2240 -8.26 0.00687 3.6500 3.51000 7.150
## 7 7 0.2360 -6.62 0.02380 2.1300 1.98000 5.120
## 8 8 0.2390 -5.56 0.03180 1.2800 1.11000 3.760
## 9 9 0.2400 -4.73 0.03670 0.7920 0.63300 2.810
## 10 10 0.2390 -4.11 0.03920 0.5040 0.36600 2.130
## 11 12 0.2630 -3.54 0.14400 0.2220 0.12500 1.260
## 12 14 0.2500 -3.01 0.11600 0.1080 0.04430 0.767
## 13 16 0.8890 -1.32 0.85800 0.0569 0.01690 0.476
## 14 18 0.8650 -1.19 0.85000 0.0320 0.00625 0.301
## 15 20 0.8090 -1.14 0.79900 0.0189 0.00235 0.201
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 81 26 16 15 14
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $turquoise
## [1] "RPL13" "RPLP2" "RPL41" "RPS12" "RPS2" "RPL3" "RPL13A"
## [8] "JUN" "FOSB" "FOS" "JUNB" "IER2" "DUSP1" "DNAJA1"
## [15] "TNFAIP3" "MALAT1" "IFRD1" "DDX3Y" "NAMPT" "EGR1" "EIF4A3"
## [22] "SLC2A3" "SLC10A1" "RGCC" "ANXA1" "TUBA1A"
##
## $brown
## [1] "INPP4B" "CAMK4" "SERINC5" "ANK3" "PAG1" "ARHGAP15"
## [7] "CDC14A" "MGAT5" "THEMIS" "HIVEP2" "TNFAIP8" "CD44"
## [13] "ADAM19" "TNIK" "PVT1"
##
## $blue
## [1] "ZEB2" "C1orf21" "AOAH" "TGFBR3" "GNLY"
## [6] "PPP2R2B" "OSBPL5" "SYNE1" "AC243829.2" "NCALD"
## [11] "KLRC3" "SETBP1" "KLRD1" "SGCD" "LYN"
## [16] "KLRK1" "ADGRG5" "VAV3" "KLRF1" "LINC02384"
## [21] "CTBP2" "IKZF2" "NCAM1" "PDGFD" "AC093865.1"
## [26] "PRSS23" "EPB41L4A" "CCL5" "ABCB1" "MYBL1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "RPL13" "RPLP2" "RPL41" "RPS12" "RPS2" "RPL3" "RPL13A"
## [8] "JUN" "FOSB" "FOS" "JUNB" "IER2" "DUSP1" "DNAJA1"
## [15] "TNFAIP3" "MALAT1" "IFRD1" "DDX3Y" "NAMPT" "EGR1" "EIF4A3"
## [22] "SLC2A3" "SLC10A1" "RGCC" "ANXA1" "TUBA1A"
##
## $brown
## [1] "INPP4B" "CAMK4" "SERINC5" "ANK3" "PAG1" "ARHGAP15"
## [7] "CDC14A" "MGAT5" "THEMIS" "HIVEP2" "TNFAIP8" "CD44"
## [13] "ADAM19" "TNIK" "PVT1"
##
## $blue
## [1] "ZEB2" "C1orf21" "AOAH" "TGFBR3" "GNLY"
## [6] "PPP2R2B" "OSBPL5" "SYNE1" "AC243829.2" "NCALD"
## [11] "KLRC3" "SETBP1" "KLRD1" "SGCD" "LYN"
## [16] "KLRK1" "ADGRG5" "VAV3" "KLRF1" "LINC02384"
## [21] "CTBP2" "IKZF2" "NCAM1" "PDGFD" "AC093865.1"
## [26] "PRSS23" "EPB41L4A" "CCL5" "ABCB1" "MYBL1"
##
## [1] "5026_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8736## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.0588e-15
## PC_ 1
## Positive: ARHGAP15, RORA, SKAP1, PAG1, SOS1, LINC01619, GPRIN3, DPYD, FRY, RABGAP1L
## ADAM19, RUNX2, INPP4B, CHST11, CDC14A, ZBTB20, FOXO1, PPP3CA, PPP1R16B, NIBAN1
## Negative: RPL13, RPLP2, RPLP1, RPS18, RPL41, RPS19, RPS23, RPS28, RPS27A, RPS12
## RPS2, FOS, JUN, FOSB, IER2, AC022217.3, AL691403.1, AC103591.3, EGR1, EIF4A3
## PC_ 2
## Positive: LINC02694, IKZF2, AC093865.1, TOX, IL2RA, TTN, CCDC141, HPGD, RTKN2, AC013652.1
## MIR4435-2HG, CYTOR, DUSP4, STAM, ENTPD1, PALM2-AKAP2, NIBAN1, ST8SIA6, GPR55, RGS1
## Negative: ANK3, BACH2, PRKCA, NELL2, RASGRF2, NR3C2, PCSK5, BTBD11, PELI2, RBMS1
## UST, PDE4D, PRKN, IGF1R, SBF2, APBA2, EDA, MGAT5, THEMIS, ITGA4
## PC_ 3
## Positive: PDE4D, PLCB1, FRY, ADAM12, LINC00299, LATS2, PTPN13, AL136456.1, ABCB1, NCALD
## SYTL2, MYBL1, TNFAIP3, AGAP1, RUNX2, AUTS2, SLC4A10, PPP2R2B, KIF5C, ZEB2
## Negative: LEF1, FOXP1, UBASH3B, ARID5B, MAN2A1, ICOS, TSHZ2, MAML2, APBA2, SLC9A9
## CMTM8, AC139720.1, SESN3, FAAH2, CERS6, AL353660.1, SLC22A23, FHIT, FKBP5, AC233976.1
## PC_ 4
## Positive: RUNX1, AOAH, UBASH3B, PPP1R16B, LYN, ZFPM1, ZEB2, CMTM8, C1orf21, TSHZ2
## ETV6, BTBD11, GRK5, ATXN7L1, PRR5L, DISC1, IFNG-AS1, KIAA1671, ADCY9, SGCD
## Negative: FOSB, FOS, RPS2, JUN, RPS28, AC022217.3, RPS19, RPL41, RPS23, RPS12
## RPLP1, RPS18, RPL13, DNAJA1, RPLP2, RPS27A, PLCG2, IER2, EIF4A3, TEX14
## PC_ 5
## Positive: AL136456.1, IL2RA, BCL2, IKZF2, HPGD, PLCL1, AC093865.1, LDLRAD4, ADAM12, IGF1R
## PTPN13, RTKN2, AL589693.1, CR1, SAMD12, FAM13A, DST, CCDC141, GPR55, ENTPD1
## Negative: TGFBR3, ZEB2, PRR5L, SLF1, C1orf21, AOAH, NR3C1, TPRG1, ANXA1, KLRK1
## PDGFD, FOSB, EDARADD, SAMD3, ANK3, RAB27B, TBXAS1, PPP1R16B, ARHGAP26, IFNG-AS1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00884 -3.74 0.88400 101.0000 1.01e+02 106.000
## 2 2 0.24200 -11.10 0.85700 51.7000 5.14e+01 57.900
## 3 3 0.74500 -15.20 0.86500 26.8000 2.64e+01 32.000
## 4 4 0.63900 -11.20 0.71500 14.0000 1.38e+01 17.900
## 5 5 0.62000 -8.34 0.71600 7.4200 7.23e+00 10.200
## 6 6 0.64900 -4.86 0.83400 3.9800 3.80e+00 5.840
## 7 7 0.70100 -3.82 0.61600 2.1700 2.02e+00 3.690
## 8 8 0.21600 -7.69 -0.00302 1.2100 1.09e+00 2.640
## 9 9 0.67500 -3.04 0.75800 0.6890 5.92e-01 1.990
## 10 10 0.12400 -3.56 0.06370 0.4030 3.22e-01 1.550
## 11 12 0.17700 -3.16 0.02010 0.1530 1.00e-01 0.992
## 12 14 0.08760 -1.75 0.06620 0.0670 3.07e-02 0.659
## 13 16 0.12300 -1.76 -0.00561 0.0337 9.71e-03 0.446
## 14 18 0.61400 -1.01 0.98100 0.0189 3.08e-03 0.304
## 15 20 0.07170 -1.06 0.05750 0.0114 1.03e-03 0.208
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 1 2 3 4 5 6 7 8 9
## 57 28 24 19 19 15 14 13 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 7 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 7 module eigengenes in given set.## $green
## [1] "ARHGAP15" "PAG1" "SOS1" "LINC01619" "GPRIN3"
## [6] "DPYD" "ADAM19" "INPP4B" "CDC14A" "ZBTB20"
## [11] "FOXO1" "PPP3CA" "MBNL1" "MGAT5" "DOCK10"
## [16] "ANK3" "BACH2" "PRKCA" "NELL2" "RASGRF2"
## [21] "NR3C2" "UST" "APBA2" "EDA" "THEMIS"
## [26] "ITGA4" "GREM2" "SAMD12" "LEF1" "FOXP1"
## [31] "UBASH3B" "ARID5B" "MAN2A1" "ICOS" "TSHZ2"
## [36] "MAML2" "SLC9A9" "CMTM8" "AC139720.1" "SESN3"
## [41] "FAAH2" "CERS6" "AL353660.1" "SLC22A23" "FHIT"
## [46] "FKBP5" "AC233976.1" "PLCL1" "MLLT3" "RUNX1"
## [51] "ZFPM1" "ETV6" "PRR5L" "DISC1" "IFNG-AS1"
## [56] "ADCY9" "GNAO1" "AL589693.1" "CR1" "FAM13A"
## [61] "PLXNA4" "TPRG1" "EDARADD" "SAMD3" "KIAA0825"
## [66] "LINC01934" "LINC02384" "KCNQ5" "TIAM1" "GAB2"
## [71] "EEPD1" "CSGALNACT1" "ACVR2A" "LINC00511" "CYSLTR1"
## [76] "TRIM2"
##
## $brown
## [1] "RORA" "FRY" "RUNX2" "TANK" "IGF1R"
## [6] "PCSK5" "BTBD11" "PELI2" "RBMS1" "PDE4D"
## [11] "PRKN" "SBF2" "SATB1-AS1" "PLCB1" "ADAM12"
## [16] "LINC00299" "LATS2" "PTPN13" "AL136456.1" "ABCB1"
## [21] "NCALD" "SYTL2" "MYBL1" "AGAP1" "AUTS2"
## [26] "SLC4A10" "PPP2R2B" "KIF5C" "MSC-AS1" "ELOVL4"
## [31] "BCL2" "DST" "ABCA1" "MCTP2"
##
## $pink
## [1] "SKAP1" "RABGAP1L" "CHST11" "PPP1R16B" "KIAA1671" "TGFBR3"
## [7] "SLF1" "NR3C1" "RAB27B" "TBXAS1" "SEMA5A" "SNED1"
## [13] "FGF14"
##
## $yellow
## [1] "NIBAN1" "PDE4B" "LINC02694" "IKZF2" "AC093865.1"
## [6] "TOX" "IL2RA" "TTN" "CCDC141" "HPGD"
## [11] "RTKN2" "AC013652.1" "DUSP4" "STAM" "RGS1"
## [16] "MIR181A1HG" "GBP5" "ATXN7L1" "LDLRAD4"
##
## $black
## [1] "RPL13" "RPLP2" "RPLP1" "RPS18" "RPL41"
## [6] "RPS19" "RPS23" "RPS28" "RPS27A" "RPS12"
## [11] "RPS2" "AC103591.3" "SH3RF3" "PLCG2"
##
## $red
## [1] "FOS" "JUN" "FOSB" "IER2" "AC022217.3"
## [6] "AL691403.1" "EGR1" "EIF4A3" "TEX14" "CSKMT"
## [11] "DNAJA1" "TNFAIP3" "ID2" "ANXA1" "AL360012.1"
##
## $blue
## [1] "MIR4435-2HG" "CYTOR" "ENTPD1" "PALM2-AKAP2" "ST8SIA6"
## [6] "GPR55" "MYB" "BARD1" "CENPE" "ZEB2"
## [11] "GRK5" "SLC16A10" "AOAH" "LYN" "C1orf21"
## [16] "SGCD" "PDGFD" "SETBP1" "KLRK1" "ARHGAP26"
## [21] "GNLY" "VAV3" "ADGRG1" "CTBP2" "SLC4A4"
## [26] "TMCC3" "DAPK2" "ITGAX"
##
## [1] "128/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "751/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "101/10000 permutations failed the Mann-Whitney test."
## $green
## [1] "ARHGAP15" "PAG1" "SOS1" "LINC01619" "GPRIN3"
## [6] "DPYD" "ADAM19" "INPP4B" "CDC14A" "ZBTB20"
## [11] "FOXO1" "PPP3CA" "MBNL1" "MGAT5" "DOCK10"
## [16] "ANK3" "BACH2" "PRKCA" "NELL2" "RASGRF2"
## [21] "NR3C2" "UST" "APBA2" "EDA" "THEMIS"
## [26] "ITGA4" "GREM2" "SAMD12" "LEF1" "FOXP1"
## [31] "UBASH3B" "ARID5B" "MAN2A1" "ICOS" "TSHZ2"
## [36] "MAML2" "SLC9A9" "CMTM8" "AC139720.1" "SESN3"
## [41] "FAAH2" "CERS6" "AL353660.1" "SLC22A23" "FHIT"
## [46] "FKBP5" "AC233976.1" "PLCL1" "MLLT3" "RUNX1"
## [51] "ZFPM1" "ETV6" "PRR5L" "DISC1" "IFNG-AS1"
## [56] "ADCY9" "GNAO1" "AL589693.1" "CR1" "FAM13A"
## [61] "PLXNA4" "TPRG1" "EDARADD" "SAMD3" "KIAA0825"
## [66] "LINC01934" "LINC02384" "KCNQ5" "TIAM1" "GAB2"
## [71] "EEPD1" "CSGALNACT1" "ACVR2A" "LINC00511" "CYSLTR1"
## [76] "TRIM2"
##
## $brown
## [1] "RORA" "FRY" "RUNX2" "TANK" "IGF1R"
## [6] "PCSK5" "BTBD11" "PELI2" "RBMS1" "PDE4D"
## [11] "PRKN" "SBF2" "SATB1-AS1" "PLCB1" "ADAM12"
## [16] "LINC00299" "LATS2" "PTPN13" "AL136456.1" "ABCB1"
## [21] "NCALD" "SYTL2" "MYBL1" "AGAP1" "AUTS2"
## [26] "SLC4A10" "PPP2R2B" "KIF5C" "MSC-AS1" "ELOVL4"
## [31] "BCL2" "DST" "ABCA1" "MCTP2"
##
## $yellow
## [1] "NIBAN1" "PDE4B" "LINC02694" "IKZF2" "AC093865.1"
## [6] "TOX" "IL2RA" "TTN" "CCDC141" "HPGD"
## [11] "RTKN2" "AC013652.1" "DUSP4" "STAM" "RGS1"
## [16] "MIR181A1HG" "GBP5" "ATXN7L1" "LDLRAD4"
##
## $black
## [1] "RPL13" "RPLP2" "RPLP1" "RPS18" "RPL41"
## [6] "RPS19" "RPS23" "RPS28" "RPS27A" "RPS12"
## [11] "RPS2" "AC103591.3" "SH3RF3" "PLCG2"
##
## $red
## [1] "FOS" "JUN" "FOSB" "IER2" "AC022217.3"
## [6] "AL691403.1" "EGR1" "EIF4A3" "TEX14" "CSKMT"
## [11] "DNAJA1" "TNFAIP3" "ID2" "ANXA1" "AL360012.1"
##
## $blue
## [1] "MIR4435-2HG" "CYTOR" "ENTPD1" "PALM2-AKAP2" "ST8SIA6"
## [6] "GPR55" "MYB" "BARD1" "CENPE" "ZEB2"
## [11] "GRK5" "SLC16A10" "AOAH" "LYN" "C1orf21"
## [16] "SGCD" "PDGFD" "SETBP1" "KLRK1" "ARHGAP26"
## [21] "GNLY" "VAV3" "ADGRG1" "CTBP2" "SLC4A4"
## [26] "TMCC3" "DAPK2" "ITGAX"
##
## [1] "5026_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5932## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50095## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.4361e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ARHGAP15, RORA, DPYD, MBNL1, NEK7, CDC14A, PAM, SAMSN1, BBS9, NR3C1
## PPP3CA, RNF19A, ZFAND6, TANK, MDFIC, CBLB, FTO, FRY, RBMS1, CNOT6L
## Negative: RPL13A, RPL38, RPL13, RPL28, RPLP2, RPLP1, RPS18, RPS23, EEF1A1, RPS11
## RPS19, RPS12, RPL37, RPS28, RPL23A, RPL41, RPL37A, RPS2, JUN, FOSB
## PC_ 2
## Positive: LINC02694, IKZF2, TTN, RTKN2, IL2RA, AC093865.1, CCDC141, TOX, CDHR3, STAM
## HPGD, AC013652.1, ST8SIA6, ENTPD1, PALM2-AKAP2, MIR4435-2HG, CYTOR, RBBP8, ATXN7L1, JAZF1
## Negative: ANK3, BACH2, PRKCA, NELL2, NR3C2, RASGRF2, RBMS1, PDE4D, THEMIS, INPP4B
## FRY, PABPC1, BTBD11, FKBP5, PLCB1, STAT4, UST, PELI2, PCSK5, EDA
## PC_ 3
## Positive: DUSP1, RPS2, JUN, FOSB, DNAJA1, FOS, RPS28, RPL13, RPL41, RPS23
## RPL28, RPS19, RPLP1, LTB, RPLP2, JUNB, RPS18, RPS12, EEF1A1, NEU1
## Negative: BTBD11, SLCO3A1, ADAM19, ADAM12, FRY, MYBL1, GRAP2, PTPN13, STX18-AS1, GALNT10
## PIN4, SIDT1, PPP1R16B, AL136962.1, LINC00299, PPP2R2B, LINC02649, PLCB1, GRAMD1B, BCL2
## PC_ 4
## Positive: C1orf21, ZEB2, FAM49A, AOAH, DOCK5, SAMD3, KLRF1, AGAP1, SYTL2, KLRK1
## OSBPL5, SPON2, LINC02384, CD8B, SGCD, TRIO, KIAA1671, DTHD1, MCTP2, PLCB1
## Negative: TSHZ2, INPP4B, PLCL1, ARID5B, SESN3, CMTM8, ICOS, ACVR2A, GCNT4, AL353660.1
## TTC39B, CYSLTR1, FMN1, PRKCA, LINC01550, MAN1C1, TIAM1, CSGALNACT1, AC139720.1, SELL
## PC_ 5
## Positive: AOAH, C1orf21, KLRK1, FAM49A, ZEB2, SPON2, SGCD, KLRF1, KIAA1671, TPRG1
## OSBPL5, UTY, SLF1, DOCK5, MTSS1, USP9Y, KDM5D, SNTB1, GNAO1, AC243829.2
## Negative: AL136456.1, ADAM12, PDE4D, CCR6, BCL2, PTPN13, EDA, MAP3K4, LINC00299, RORA
## MB21D2, IL2RA, LDLRAD4, FRY, DUSP16, PLCB1, ARHGEF7, MAN1A1, SLC4A10, TNFRSF11A
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.014300 -5.950 0.905 130.0000 1.30e+02 135.000
## 2 2 0.005390 1.580 0.813 66.9000 6.66e+01 72.500
## 3 3 0.000218 -0.191 0.795 34.9000 3.46e+01 39.800
## 4 4 0.069100 -2.330 0.859 18.4000 1.82e+01 22.900
## 5 5 0.215000 -2.940 0.855 9.8900 9.66e+00 13.700
## 6 6 0.397000 -3.060 0.708 5.4100 5.15e+00 8.670
## 7 7 0.646000 -2.980 0.796 3.0200 2.79e+00 5.740
## 8 8 0.845000 -2.740 0.890 1.7300 1.52e+00 3.980
## 9 9 0.931000 -2.460 0.936 1.0200 8.40e-01 2.870
## 10 10 0.925000 -2.210 0.908 0.6200 4.71e-01 2.140
## 11 12 0.914000 -1.830 0.896 0.2520 1.49e-01 1.270
## 12 14 0.922000 -1.520 0.905 0.1160 4.90e-02 0.796
## 13 16 0.940000 -1.350 0.928 0.0599 1.67e-02 0.516
## 14 18 0.981000 -1.200 0.977 0.0334 5.91e-03 0.344
## 15 20 0.957000 -1.220 0.968 0.0198 2.16e-03 0.259
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 195 17 17 14 13
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "RPL13A" "RPL38" "RPL13" "RPL28" "RPLP2"
## [6] "RPLP1" "RPS18" "RPS23" "EEF1A1" "RPS11"
## [11] "RPS19" "RPS12" "RPL37" "RPS28" "RPL23A"
## [16] "RPL41" "RPL37A" "RPS2" "JUN" "FOSB"
## [21] "LTB" "FOS" "JUNB" "ERCC1" "IER2"
## [26] "DUSP1" "DNAJA1" "NEU1" "AC022217.3" "IFRD1"
## [31] "GALM"
##
## $yellow
## [1] "IKZF2" "TTN" "RTKN2" "IL2RA" "AC093865.1"
## [6] "CCDC141" "TOX" "CDHR3" "STAM" "HPGD"
## [11] "ST8SIA6" "ATXN7L1" "JAZF1"
##
## $turquoise
## [1] "STIL" "KNL1" "ECT2" "TOP2A" "PCLAF"
## [6] "CCNF" "RECQL4" "RAD51" "WDR62" "SPC24"
## [11] "KIF18B" "TYMS" "MND1" "AC000065.1" "ESCO2"
## [16] "BRCA2" "ANLN"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "RPL13A" "RPL38" "RPL13" "RPL28" "RPLP2"
## [6] "RPLP1" "RPS18" "RPS23" "EEF1A1" "RPS11"
## [11] "RPS19" "RPS12" "RPL37" "RPS28" "RPL23A"
## [16] "RPL41" "RPL37A" "RPS2" "JUN" "FOSB"
## [21] "LTB" "FOS" "JUNB" "ERCC1" "IER2"
## [26] "DUSP1" "DNAJA1" "NEU1" "AC022217.3" "IFRD1"
## [31] "GALM"
##
## $yellow
## [1] "IKZF2" "TTN" "RTKN2" "IL2RA" "AC093865.1"
## [6] "CCDC141" "TOX" "CDHR3" "STAM" "HPGD"
## [11] "ST8SIA6" "ATXN7L1" "JAZF1"
##
## $turquoise
## [1] "STIL" "KNL1" "ECT2" "TOP2A" "PCLAF"
## [6] "CCNF" "RECQL4" "RAD51" "WDR62" "SPC24"
## [11] "KIF18B" "TYMS" "MND1" "AC000065.1" "ESCO2"
## [16] "BRCA2" "ANLN"
##
## [1] "5020_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.646## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50091## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.2953e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: KLF12, ARHGAP15, MBNL1, LINC01619, USP15, ZBTB20, PAG1, IQGAP2, SLC38A1, EXOC4
## DPYD, CBLB, FBXW7, ITGB1, RAP1GDS1, RORA, CAMK4, MAN1A2, FYN, FOXP1
## Negative: RPS27, RPL19, SEMA3A, PLXNA4, TEX9, ST6GALNAC3, NUP210L, AC022217.3, JUN, PIK3AP1
## ABCG2, PLAC8L1, MOB3B, H2AFJ, SGCD, TTC8, SLC2A1-AS1, SETBP1, HIST1H4C, AOAH
## PC_ 2
## Positive: ANK3, BACH2, PRKCA, NELL2, NR3C2, RBMS1, PELI2, PCSK5, UST, THEMIS
## RASGRF2, INPP4B, EDA, PRKN, IGF1R, PDE4D, BCL2, MYBL1, ZNF516, ARHGAP15
## Negative: LINC02694, TTN, IKZF2, TOX, RTKN2, CCDC141, ST8SIA6, AC093865.1, MIR4435-2HG, STAM
## CDHR3, IL2RA, ATXN7L1, CTLA4, ENTPD1, IL7, F5, HPGD, SLC16A10, GBP5
## PC_ 3
## Positive: FHIT, TSHZ2, INPP4B, GNAQ, TXK, SESN3, UBASH3B, AC139720.1, CMTM8, RPL19
## IKZF2, FOS, AL353660.1, PRKCA, FOXP1, PLCL1, RTKN2, CERS6, MALAT1, STAM
## Negative: C1orf21, ZEB2, GNLY, MVB12B, KLRK1, TGFBR3, IL18RAP, CMIP, MYBL1, AOAH
## SYTL3, SETBP1, DTHD1, PLCB1, NCALD, PPP2R2B, AUTS2, SYTL2, MSC-AS1, MAP3K8
## PC_ 4
## Positive: FOSB, JUN, AL691403.1, FOS, LINC00910, NEU1, IER2, ERCC1, DNAJA1, AC022217.3
## EGR1, AL499604.1, TUBA1A, AL360012.1, CSKMT, ARF4, DDX3X, AC253572.2, TEX14, IFRD1
## Negative: SATB1-AS1, TSHZ2, ARFIP1, AC233976.1, ARID5B, PLXNA4, PRKCB, USP6NL, AL589693.1, PRKCA
## RASSF6, FAAH2, AL122035.1, AHCYL2, AC244131.2, LINC01284, DDX60, TSPOAP1-AS1, AKAP6, AC064834.1
## PC_ 5
## Positive: AL136456.1, FRY, MCF2L2, RUNX2, LINC00299, PTPN13, MB21D2, ADAM12, CCR6, KAT2B
## AFDN, NTN4, RBMS1, PLD1, MSC-AS1, VCL, WDFY2, HLF, AC010754.1, RORA
## Negative: AOAH, C1orf21, ZEB2, DTHD1, KLRK1, RAB27B, PDGFD, GFOD1, KCNQ5, AC243829.2
## CD8B, MAP3K8, CBLB, SETBP1, ARID5B, AF165147.1, FYN, A2M-AS1, SAMD3, LINC01934
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.223 -11.20 0.624 1.08e+02 1.08e+02 115.0000
## 2 2 0.264 -6.30 0.721 5.61e+01 5.57e+01 63.9000
## 3 3 0.351 -4.94 0.784 2.94e+01 2.90e+01 35.9000
## 4 4 0.381 -4.13 0.815 1.55e+01 1.53e+01 20.4000
## 5 5 0.433 -3.65 0.881 8.25e+00 8.14e+00 11.7000
## 6 6 0.478 -3.43 0.901 4.44e+00 4.36e+00 6.8200
## 7 7 0.504 -2.65 0.932 2.42e+00 2.37e+00 4.0200
## 8 8 0.557 -2.85 0.800 1.33e+00 1.29e+00 2.5100
## 9 9 0.275 -7.00 0.180 7.43e-01 7.22e-01 1.7100
## 10 10 0.320 -6.40 0.220 4.20e-01 4.01e-01 1.2000
## 11 12 0.368 -5.28 0.247 1.41e-01 1.27e-01 0.6450
## 12 14 0.355 -5.50 0.182 5.04e-02 4.08e-02 0.3730
## 13 16 0.388 -4.98 0.251 1.94e-02 1.37e-02 0.2270
## 14 18 0.358 -4.85 0.180 8.09e-03 4.93e-03 0.1420
## 15 20 0.358 -4.29 0.187 3.64e-03 1.73e-03 0.0907
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3
## 177 13 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "KLF12" "ARHGAP15" "MBNL1" "ZBTB20" "PAG1" "EXOC4"
## [7] "DPYD" "FBXW7" "CAMK4" "FTX" "GNAQ"
##
## $turquoise
## [1] "JUN" "FOS" "FOSB" "AL691403.1" "LINC00910"
## [6] "NEU1" "IER2" "ERCC1" "DNAJA1" "EGR1"
## [11] "TUBA1A" "IFRD1" "ATP2B1-AS1"
##
## $brown
## [1] "TTN" "IKZF2" "TOX" "CCDC141" "ST8SIA6"
## [6] "AC093865.1" "MIR4435-2HG" "CDHR3" "IL2RA" "SLC16A10"
##
## [1] "42/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "KLF12" "ARHGAP15" "MBNL1" "ZBTB20" "PAG1" "EXOC4"
## [7] "DPYD" "FBXW7" "CAMK4" "FTX" "GNAQ"
##
## $turquoise
## [1] "JUN" "FOS" "FOSB" "AL691403.1" "LINC00910"
## [6] "NEU1" "IER2" "ERCC1" "DNAJA1" "EGR1"
## [11] "TUBA1A" "IFRD1" "ATP2B1-AS1"
##
## $brown
## [1] "TTN" "IKZF2" "TOX" "CCDC141" "ST8SIA6"
## [6] "AC093865.1" "MIR4435-2HG" "CDHR3" "IL2RA" "SLC16A10"
##
## [1] "5016_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6483## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50116## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.7084e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: INPP4B, MGAT5, ANK3, PRKCA, CDC14A, ARHGAP15, FOXP1, MAP3K1, PAG1, GNAQ
## MAML2, NR3C2, FKBP5, CSGALNACT1, TSHZ2, CASK, GPHN, ETV6, DUSP16, ADAM19
## Negative: AOAH, ZEB2, AC243829.2, C1orf21, SETBP1, GNLY, KLRD1, SYNE1, NCAM1, OSBPL5
## SGCD, PDGFD, VAV3, SAMD3, KLRK1, LYN, LINC02384, ARHGAP26, DTHD1, AL392086.3
## PC_ 2
## Positive: PPP2R2B, RABGAP1L, CHST11, ST6GAL1, GNG2, SAMD3, SYNE1, ATXN1, PTK2B, OSBPL3
## AC243829.2, RORA, LPP, LINC02384, JAZF1, RAB27A, LINC01619, ARHGAP26, SUSD1, ZEB2
## Negative: RPL13, RPLP2, RPS2, RPL41, RPS16, RPS27, JUN, FOS, JUNB, FOSB
## CRIP1, TRBC2, AC022217.3, UBE2E2, ADAMTS17, AC087286.2, PTK2, PARD3B, KANK1, ANXA1
## PC_ 3
## Positive: LINC02694, AC013652.1, RTKN2, IKZF2, STAM, EZH2, JUN, HPGD, TTN, AC022217.3
## NAMPT, FOSB, MIR181A1HG, FOS, ATP2B1-AS1, AC093865.1, CCDC141, IER2, CDHR3, ENTPD1
## Negative: ANK3, ITGA4, BTBD11, NR3C2, PRKCB, BACH2, PELI2, NELL2, TRABD2A, PCSK5
## MAML2, PRKN, ARHGAP5, THEMIS, FKBP5, MCTP2, WNT7A, SNTB1, UST, PLCB1
## PC_ 4
## Positive: PFKFB3, ADAM19, BRCA2, FRY, MKI67, ADAM12, PTPN13, WWC2, COL5A3, RUNX2
## ATAD5, BTBD11, E2F7, CEP112, IL2RA, ANK1, CR1, NCAPG2, SLCO3A1, CDC45
## Negative: RPS2, RPLP2, RPL41, RPS16, RPS27, FOSB, RPL13, JUN, FOS, JUNB
## AC022217.3, DNAJA1, ZNF407, TUBA1A, IFRD1, PZP, TRBC2, ANXA1, TTTY14, ZNF451-AS1
## PC_ 5
## Positive: LRRIQ3, MKI67, CDC45, E2F7, DIAPH3, BRCA2, ASPM, BRIP1, MELK, SMC2
## BRCA1, CENPU, ADAM28, AC005400.1, ILDR2, ECT2, NCAPG2, RCAN2, DMPK, GAS2L3
## Negative: LINC02694, HPGD, MIR4435-2HG, AC013652.1, CTLA4, TTN, ST6GAL1, BCL2L11, RTKN2, RUNX2
## CDHR3, AC011997.1, CCDC141, COMMD1, MIR181A1HG, TNFRSF11A, ZNF365, MECR, ENTPD1, TGFBR3
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.131 -12.80 0.669 94.3000 94.30000 98.600
## 2 2 0.276 -11.00 0.801 48.8000 48.80000 54.500
## 3 3 0.483 -8.46 0.825 25.6000 25.50000 31.700
## 4 4 0.272 -17.60 0.133 13.7000 13.50000 19.600
## 5 5 0.292 -12.30 0.153 7.4800 7.21000 12.900
## 6 6 0.320 -9.46 0.185 4.1800 3.91000 9.010
## 7 7 0.376 -10.50 0.223 2.3900 2.14000 6.670
## 8 8 0.385 -8.62 0.245 1.4100 1.17000 5.160
## 9 9 0.415 -8.70 0.258 0.8600 0.65000 4.140
## 10 10 0.410 -7.41 0.266 0.5420 0.36900 3.400
## 11 12 0.398 -5.80 0.278 0.2390 0.12300 2.410
## 12 14 0.412 -5.55 0.266 0.1200 0.04280 1.790
## 13 16 0.398 -4.91 0.263 0.0674 0.01520 1.360
## 14 18 0.394 -4.49 0.265 0.0412 0.00572 1.050
## 15 20 0.411 -4.38 0.248 0.0267 0.00219 0.825
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 1 2 3 4 5
## 63 46 38 28 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $yellow
## [1] "INPP4B" "MGAT5" "ANK3" "PRKCA" "CDC14A" "ARHGAP15"
## [7] "FOXP1" "MAP3K1" "PAG1" "GNAQ" "MAML2" "TSHZ2"
## [13] "CASK" "GPHN" "DUSP16" "BACH2" "IMMP2L" "RORA"
## [19] "PARD3B" "KANK1" "NELL2" "TRABD2A" "PCSK5" "PRKN"
## [25] "ARHGAP5" "WNT7A" "PLXNA4" "CEP112"
##
## $blue
## [1] "NR3C2" "FKBP5" "CSGALNACT1" "ETV6" "ADAM19"
## [6] "RUNX2" "ZBTB20" "LPP" "LINC01619" "PARP8"
## [11] "EZH2" "ASPM" "ITGA4" "BTBD11" "THEMIS"
## [16] "LINC01934" "ZNF609" "PFKFB3" "BRCA2" "FRY"
## [21] "MKI67" "PTPN13" "E2F7" "NCAPG2" "SLCO3A1"
## [26] "CDC45" "AL589693.1" "CCR6" "MELK" "ZNF407"
## [31] "LRRIQ3" "DIAPH3" "BRIP1" "SMC2" "BRCA1"
## [36] "CENPU" "ADAM28" "AC005400.1" "ECT2" "RCAN2"
## [41] "DMPK" "GAS2L3" "PODXL" "ZGRF1" "ESCO2"
## [46] "TOP2A"
##
## $turquoise
## [1] "AOAH" "ZEB2" "AC243829.2" "C1orf21" "SETBP1"
## [6] "GNLY" "KLRD1" "SYNE1" "NCAM1" "OSBPL5"
## [11] "SGCD" "PDGFD" "VAV3" "SAMD3" "KLRK1"
## [16] "LYN" "LINC02384" "ARHGAP26" "DTHD1" "AL392086.3"
## [21] "LGR6" "TGFBR3" "LRFN2" "KLRF1" "ADGRG5"
## [26] "PPP2R2B" "GNG2" "ATXN1" "JAZF1" "SYTL2"
## [31] "SGMS1" "LINC02694" "AC013652.1" "RTKN2" "IKZF2"
## [36] "STAM" "HPGD" "TTN" "MIR181A1HG" "AC093865.1"
## [41] "CCDC141" "CDHR3" "ENTPD1" "IL2RA" "MCTP2"
## [46] "SNTB1" "PLCB1" "ADAM12" "WWC2" "COL5A3"
## [51] "ANK1" "CR1" "ZMIZ1" "PZP" "KCNQ5"
## [56] "CTLA4" "AC011997.1" "COMMD1" "TNFRSF11A" "ZNF365"
## [61] "CSF2RB" "LINC00426" "AL096794.1"
##
## $green
## [1] "RABGAP1L" "CHST11" "ST6GAL1" "PTK2B" "OSBPL3"
## [6] "RAB27A" "SUSD1" "PRKCB" "MIR4435-2HG" "BCL2L11"
## [11] "MECR"
##
## $brown
## [1] "RPL13" "RPLP2" "RPS2" "RPL41" "RPS16"
## [6] "RPS27" "JUN" "FOS" "JUNB" "FOSB"
## [11] "CRIP1" "TRBC2" "AC022217.3" "UBE2E2" "ADAMTS17"
## [16] "AC087286.2" "PTK2" "ANXA1" "DNAJA1" "TUBA1A"
## [21] "ATP8B1" "ATP2B1-AS1" "NAMPT" "IER2" "LMNA"
## [26] "RGS1" "PELI2" "UST" "ZNF516" "TAFA1"
## [31] "ATAD5" "STIMATE" "IFRD1" "TTTY14" "ZNF451-AS1"
## [36] "TNFAIP3" "YPEL5" "ILDR2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "3/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1233/10000 permutations failed the Mann-Whitney test."
## [1] "19/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "INPP4B" "MGAT5" "ANK3" "PRKCA" "CDC14A" "ARHGAP15"
## [7] "FOXP1" "MAP3K1" "PAG1" "GNAQ" "MAML2" "TSHZ2"
## [13] "CASK" "GPHN" "DUSP16" "BACH2" "IMMP2L" "RORA"
## [19] "PARD3B" "KANK1" "NELL2" "TRABD2A" "PCSK5" "PRKN"
## [25] "ARHGAP5" "WNT7A" "PLXNA4" "CEP112"
##
## $blue
## [1] "NR3C2" "FKBP5" "CSGALNACT1" "ETV6" "ADAM19"
## [6] "RUNX2" "ZBTB20" "LPP" "LINC01619" "PARP8"
## [11] "EZH2" "ASPM" "ITGA4" "BTBD11" "THEMIS"
## [16] "LINC01934" "ZNF609" "PFKFB3" "BRCA2" "FRY"
## [21] "MKI67" "PTPN13" "E2F7" "NCAPG2" "SLCO3A1"
## [26] "CDC45" "AL589693.1" "CCR6" "MELK" "ZNF407"
## [31] "LRRIQ3" "DIAPH3" "BRIP1" "SMC2" "BRCA1"
## [36] "CENPU" "ADAM28" "AC005400.1" "ECT2" "RCAN2"
## [41] "DMPK" "GAS2L3" "PODXL" "ZGRF1" "ESCO2"
## [46] "TOP2A"
##
## $turquoise
## [1] "AOAH" "ZEB2" "AC243829.2" "C1orf21" "SETBP1"
## [6] "GNLY" "KLRD1" "SYNE1" "NCAM1" "OSBPL5"
## [11] "SGCD" "PDGFD" "VAV3" "SAMD3" "KLRK1"
## [16] "LYN" "LINC02384" "ARHGAP26" "DTHD1" "AL392086.3"
## [21] "LGR6" "TGFBR3" "LRFN2" "KLRF1" "ADGRG5"
## [26] "PPP2R2B" "GNG2" "ATXN1" "JAZF1" "SYTL2"
## [31] "SGMS1" "LINC02694" "AC013652.1" "RTKN2" "IKZF2"
## [36] "STAM" "HPGD" "TTN" "MIR181A1HG" "AC093865.1"
## [41] "CCDC141" "CDHR3" "ENTPD1" "IL2RA" "MCTP2"
## [46] "SNTB1" "PLCB1" "ADAM12" "WWC2" "COL5A3"
## [51] "ANK1" "CR1" "ZMIZ1" "PZP" "KCNQ5"
## [56] "CTLA4" "AC011997.1" "COMMD1" "TNFRSF11A" "ZNF365"
## [61] "CSF2RB" "LINC00426" "AL096794.1"
##
## $brown
## [1] "RPL13" "RPLP2" "RPS2" "RPL41" "RPS16"
## [6] "RPS27" "JUN" "FOS" "JUNB" "FOSB"
## [11] "CRIP1" "TRBC2" "AC022217.3" "UBE2E2" "ADAMTS17"
## [16] "AC087286.2" "PTK2" "ANXA1" "DNAJA1" "TUBA1A"
## [21] "ATP8B1" "ATP2B1-AS1" "NAMPT" "IER2" "LMNA"
## [26] "RGS1" "PELI2" "UST" "ZNF516" "TAFA1"
## [31] "ATAD5" "STIMATE" "IFRD1" "TTTY14" "ZNF451-AS1"
## [36] "TNFAIP3" "YPEL5" "ILDR2"
##
## [1] "5035_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8223## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50218## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.3085e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: ZEB2, AOAH, C1orf21, GNLY, OSBPL5, LYN, KLRD1, PDGFD, SGCD, TGFBR3
## KLRC3, IKZF2, CTBP2, SETBP1, AC243829.2, TPST2, AGAP1, AC093865.1, MCTP2, NCAM1
## Negative: INPP4B, PAG1, CAMK4, ANK3, CDC14A, ARHGAP15, PRKCA, LEF1, ADAM19, BCL2
## TTC39C, MGAT5, MAP3K1, MDFIC, HIVEP2, GNAQ, NR3C2, FOXP1, DOCK10, AC139720.1
## PC_ 2
## Positive: PARP8, MCTP2, CBLB, MYBL1, TGFBR3, C1orf21, KLF12, RORA, SAMD3, NCALD
## ZEB2, PCNX1, CHST11, ARHGAP26, JAZF1, PPP3CA, ABCB1, AOAH, SYTL2, PPP2R2B
## Negative: RPL13, RPLP2, RPL34, RPL28, RPL13A, RPS19, TMSB10, RPL41, RPL38, RPS28
## JUN, RPL3, RPLP1, RPS18, FOS, RPS8, RPS2, RPS12, RPL18A, FOSB
## PC_ 3
## Positive: JUN, FOSB, FOS, JUNB, IER2, AC079793.1, AC022217.3, RPS2, TUBA1A, RPLP1
## RPL41, TEX14, RPS12, NAMPT, RPL3, EGR1, RPLP2, RPL13, IFRD1, RPL18A
## Negative: ADAM19, PAG1, MFHAS1, CHST11, GRAMD1B, ADAMTS17, ERN1, TIAM1, ZMIZ1-AS1, KANK1
## LINC02649, SASH1, ATXN7L1, UBASH3B, PACSIN2, ATF7IP2, EGLN3, FRY, LINC01550, CLIC5
## PC_ 4
## Positive: PLCB1, BTBD11, BACH2, IGF1R, MYBL1, ITGA4, PELI2, DPP4, GREM2, RASGRF2
## PDE4D, PCSK5, ADAM23, NELL2, ALOX5, ZNF516, TXK, MCTP2, RNF157, BCL2
## Negative: LINC02694, TTN, TOX, SNED1, CCDC141, CDHR3, RTKN2, AC013652.1, ENTPD1, STAM
## DLEU2, SEMA5A, F5, SPSB1, CYTOR, LINC01362, ST8SIA4, ZC2HC1A, CD109, MIR4435-2HG
## PC_ 5
## Positive: ST8SIA1, IFNG-AS1, MAN2A1, SESN3, UBASH3B, AL353660.1, ARID5B, FHIT, TXK, CERS6
## FOXP1, LEF1, SNTB1, MAML2, LINC01934, NELL2, AC139720.1, DOCK10, LINC01550, DISC1
## Negative: FRY, PTPN13, AL136456.1, COL5A3, MCF2L2, MSC-AS1, SASH1, PDE4D, LINC00299, RUNX2
## IL1R1, ADAM12, LINC01644, CCR6, NEDD4L, NCAPG2, ALOX5, KAT2B, B4GALT5, LINC02694
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.277 -24.70 0.84000 112.0000 1.11e+02 119.000
## 2 2 0.402 -14.10 0.76500 57.9000 5.75e+01 66.200
## 3 3 0.385 -8.30 0.81800 30.6000 3.04e+01 37.800
## 4 4 0.410 -5.53 0.79400 16.4000 1.63e+01 22.100
## 5 5 0.549 -4.07 0.88200 9.0000 8.95e+00 13.100
## 6 6 0.599 -3.12 0.78400 5.0300 4.87e+00 8.160
## 7 7 0.745 -3.32 0.87400 2.8700 2.70e+00 5.660
## 8 8 0.889 -3.06 0.96800 1.6700 1.50e+00 4.050
## 9 9 0.905 -2.74 0.94000 1.0000 8.52e-01 2.970
## 10 10 0.897 -2.55 0.90300 0.6130 4.89e-01 2.210
## 11 12 0.828 -2.19 0.78000 0.2470 1.63e-01 1.290
## 12 14 0.302 -3.42 0.17900 0.1100 5.67e-02 0.851
## 13 16 0.229 -2.59 0.00927 0.0531 1.99e-02 0.606
## 14 18 0.199 -3.29 -0.01260 0.0279 7.24e-03 0.447
## 15 20 0.327 -3.49 0.21600 0.0157 2.62e-03 0.339
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5
## 127 30 22 14 14 12
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "ZEB2" "AOAH" "C1orf21" "GNLY" "OSBPL5"
## [6] "LYN" "SGCD" "TGFBR3" "KLRC3" "IKZF2"
## [11] "SETBP1" "TPST2" "AGAP1" "AC093865.1" "NCAM1"
## [16] "SAMD3" "PRSS23" "GAS7" "PARP8" "CBLB"
## [21] "MYBL1" "NCALD" "ARHGAP26" "JAZF1" "ABCB1"
## [26] "SYTL2" "PPP2R2B" "PLCB1" "MIR4435-2HG" "TPRG1"
## [31] "DOCK5" "EFNA5" "ARHGEF28" "DGKK"
##
## $brown
## [1] "INPP4B" "PAG1" "CAMK4" "ANK3" "CDC14A"
## [6] "ARHGAP15" "PRKCA" "LEF1" "ADAM19" "BCL2"
## [11] "TTC39C" "MGAT5" "MAP3K1" "MDFIC" "HIVEP2"
## [16] "GNAQ" "NR3C2" "DOCK10" "AC139720.1" "MAML2"
## [21] "DPP4" "CMTM8" "TAB2" "KANK1" "TXK"
## [26] "PDE4B" "DISC1" "THEMIS"
##
## $turquoise
## [1] "RPL13" "RPLP2" "RPL34" "RPL28" "RPL13A"
## [6] "RPS19" "TMSB10" "RPL41" "RPL38" "RPS28"
## [11] "JUN" "RPL3" "RPLP1" "RPS18" "FOS"
## [16] "RPS8" "RPS2" "RPS12" "RPL18A" "FOSB"
## [21] "RPS23" "JUNB" "AC022217.3" "TUBA1A" "IER2"
## [26] "AC079793.1" "TEX14" "NAMPT" "EGR1" "IFRD1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "ZEB2" "AOAH" "C1orf21" "GNLY" "OSBPL5"
## [6] "LYN" "SGCD" "TGFBR3" "KLRC3" "IKZF2"
## [11] "SETBP1" "TPST2" "AGAP1" "AC093865.1" "NCAM1"
## [16] "SAMD3" "PRSS23" "GAS7" "PARP8" "CBLB"
## [21] "MYBL1" "NCALD" "ARHGAP26" "JAZF1" "ABCB1"
## [26] "SYTL2" "PPP2R2B" "PLCB1" "MIR4435-2HG" "TPRG1"
## [31] "DOCK5" "EFNA5" "ARHGEF28" "DGKK"
##
## $brown
## [1] "INPP4B" "PAG1" "CAMK4" "ANK3" "CDC14A"
## [6] "ARHGAP15" "PRKCA" "LEF1" "ADAM19" "BCL2"
## [11] "TTC39C" "MGAT5" "MAP3K1" "MDFIC" "HIVEP2"
## [16] "GNAQ" "NR3C2" "DOCK10" "AC139720.1" "MAML2"
## [21] "DPP4" "CMTM8" "TAB2" "KANK1" "TXK"
## [26] "PDE4B" "DISC1" "THEMIS"
##
## $turquoise
## [1] "RPL13" "RPLP2" "RPL34" "RPL28" "RPL13A"
## [6] "RPS19" "TMSB10" "RPL41" "RPL38" "RPS28"
## [11] "JUN" "RPL3" "RPLP1" "RPS18" "FOS"
## [16] "RPS8" "RPS2" "RPS12" "RPL18A" "FOSB"
## [21] "RPS23" "JUNB" "AC022217.3" "TUBA1A" "IER2"
## [26] "AC079793.1" "TEX14" "NAMPT" "EGR1" "IFRD1"
##
## [1] "5020_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3687## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49949## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.4344e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: RPS27, RPLP1, RPLP2, RPL41, TTN, ASTN2, XIST, TSHR, KRT72, FHIT
## LINC01259, GOLGA6L4, AL162493.1, LARGE1, AL049828.1, LMTK3, AC130324.2, PLGRKT, TNNC2, ALDH7A1
## Negative: SLC38A1, EML4, MLLT10, ATF2, ARHGAP15, KLF12, NFKB1, YPEL1, DENND1B, BABAM2
## FOXO1, STK39, MBNL1, C5orf56, BCKDHB, ATP8A1, FNDC3B, DYM, AUH, FYN
## PC_ 2
## Positive: ZEB2, KLRC3, KLRF1, SGCD, IRF8, KLRD1, AOAH, AL392086.3, OSBPL5, CTBP2
## PDGFD, C1orf21, NCALD, SETBP1, AC024028.1, IKZF2, ABI3, LYN, MTSS1, GNLY
## Negative: INPP4B, PRKCA, ANK3, CDC14A, CAMK4, TSHZ2, BCL2, LEF1, PLCL1, ARHGAP15
## PAG1, FAAH2, MAP3K1, GNAQ, IGF1R, BACH2, NELL2, FMN1, MGAT5, SNX9
## PC_ 3
## Positive: LINC02694, TOX, IL34, ST8SIA6, AC105429.1, CCDC141, SEMA3G, TTN, AC093865.1, LINC02062
## AL135978.2, ATG4C, PIGM, MCF2L2, MIR4435-2HG, CDHR3, SMC4, LINC01727, MIR181A1HG, KIF20B
## Negative: RBMS1, PDE4D, PLCB1, NFKB1, TNFAIP3, A2M, ANK3, BACH2, RPL41, RPLP1
## IGF1R, PELI2, TAFA1, RPLP2, MAP3K4, EDA, ADGRE5, LINC00612, PCSK5, NR3C2
## PC_ 4
## Positive: PLCB1, PDE4D, MYBL1, PTPN13, ADAM12, SLC4A10, LINC00299, AC104211.1, HMGCS1, CMIP
## GNG2, NTN4, MSC-AS1, NIBAN1, IL18RAP, TNFAIP3, TGFBR3, CATSPERG, MB21D2, NECTIN2
## Negative: CERS6, APBA2, LEF1, CDC7, AL392086.3, EPHX4, BHLHE40-AS1, C4orf50, SKIL, TSHZ2
## FHIT, B3GAT1, RNF43, KLRC3, ALG10, PTGDR, TXK, WDR63, KLRF1, IRF8
## PC_ 5
## Positive: AC025188.1, FOS, RPL41, JUN, LINC00513, FOSB, RORA-AS1, TRIM69, TOX, PLCG2
## RGCC, AC093583.1, RPLP1, AC013652.1, TNFRSF9, LMNA, LOXL1, RAB11A, AL691403.1, AC092640.1
## Negative: ETV6, HK1, ADAMTS17, FLACC1, PHLDB2, PNPLA1, SFMBT2, WDR64, TTLL1, FAM174B
## CELF2, MTAP, TSHZ2, PARL, ABCA10, PRR5, STX18-AS1, USP13, WWTR1, LYN
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.22400 11.500 0.5160 110.0000 1.10e+02 115.000
## 2 2 0.00131 0.338 0.5370 57.1000 5.71e+01 63.700
## 3 3 0.17200 -2.880 0.7270 30.1000 3.00e+01 36.300
## 4 4 0.34700 -3.250 0.7300 16.0000 1.59e+01 21.400
## 5 5 0.51200 -3.240 0.7090 8.6800 8.52e+00 13.100
## 6 6 0.56900 -3.200 0.6870 4.7700 4.60e+00 8.240
## 7 7 0.61800 -2.810 0.6320 2.6700 2.53e+00 5.400
## 8 8 0.70500 -2.520 0.7180 1.5200 1.40e+00 3.700
## 9 9 0.77300 -2.460 0.7210 0.8880 7.82e-01 2.620
## 10 10 0.84700 -2.350 0.8040 0.5300 4.45e-01 1.900
## 11 12 0.94200 -2.070 0.9370 0.2030 1.49e-01 1.070
## 12 14 0.85700 -1.800 0.8620 0.0868 4.98e-02 0.647
## 13 16 0.27500 -3.030 0.1370 0.0411 1.78e-02 0.409
## 14 18 0.19800 -2.310 -0.0301 0.0212 6.38e-03 0.267
## 15 20 0.23500 -2.280 0.0343 0.0118 2.48e-03 0.180
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5
## 143 19 16 13 12 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## $yellow
## [1] "EML4" "FOXO1" "DPYD" "INPP4B" "PRKCA" "ANK3" "CDC14A" "PAG1"
## [9] "FAAH2" "GNAQ" "FMN1" "MGAT5"
##
## $brown
## [1] "ARHGAP15" "NFKB1" "BCL2" "BACH2" "SNX9" "RBMS1"
## [7] "PCSK5" "PDE4D" "PLCB1" "TNFAIP3" "PELI2" "GREM2"
## [13] "RORA"
##
## $blue
## [1] "YPEL1" "ZEB2" "KLRC3" "KLRF1" "SGCD"
## [6] "IRF8" "KLRD1" "AOAH" "AL392086.3" "OSBPL5"
## [11] "CTBP2" "PDGFD" "C1orf21" "NCALD" "SETBP1"
## [16] "AC024028.1" "ABI3" "LYN" "MTSS1" "GNLY"
## [21] "B3GAT1" "SLC4A4" "PTGDR" "BHLHE40-AS1" "AC018816.1"
## [26] "AC068631.1" "CDC7" "EPHX4" "SKIL" "RNF43"
## [31] "ALG10" "WDR63" "LINC00469" "TSHZ3" "STX18-AS1"
##
## $green
## [1] "BCKDHB" "IL34" "ST8SIA6" "PIGM" "PDE1B"
## [6] "AC093583.1" "TNFRSF9" "AC092640.1" "HEATR6" "LINC02803"
## [11] "RHBDD3"
##
## [1] "275/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "63/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "EML4" "FOXO1" "DPYD" "INPP4B" "PRKCA" "ANK3" "CDC14A" "PAG1"
## [9] "FAAH2" "GNAQ" "FMN1" "MGAT5"
##
## $brown
## [1] "ARHGAP15" "NFKB1" "BCL2" "BACH2" "SNX9" "RBMS1"
## [7] "PCSK5" "PDE4D" "PLCB1" "TNFAIP3" "PELI2" "GREM2"
## [13] "RORA"
##
## $blue
## [1] "YPEL1" "ZEB2" "KLRC3" "KLRF1" "SGCD"
## [6] "IRF8" "KLRD1" "AOAH" "AL392086.3" "OSBPL5"
## [11] "CTBP2" "PDGFD" "C1orf21" "NCALD" "SETBP1"
## [16] "AC024028.1" "ABI3" "LYN" "MTSS1" "GNLY"
## [21] "B3GAT1" "SLC4A4" "PTGDR" "BHLHE40-AS1" "AC018816.1"
## [26] "AC068631.1" "CDC7" "EPHX4" "SKIL" "RNF43"
## [31] "ALG10" "WDR63" "LINC00469" "TSHZ3" "STX18-AS1"
##
## $green
## [1] "BCKDHB" "IL34" "ST8SIA6" "PIGM" "PDE1B"
## [6] "AC093583.1" "TNFRSF9" "AC092640.1" "HEATR6" "LINC02803"
## [11] "RHBDD3"saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Participant_Timepoint.rds")
results$T_TP<-paste(results$Treatment, results$Timepoint, sep="_")
results.split<-SplitObject(results, "T_TP")
#in this case just doing one documented iteration as long as the softpower is <9, otherwise setting to 8
#module set here is pretty unspectatular relative to the individual defined ones. Likely not worth analyzing further
conds<-cbind(c(5,5,4,5,5,7),c(7,8,8,8,8,8))
mods1.5<-WrapGroupModID(results.split, "NA",conds)## [1] "Bup.Nalo_0"
## PC_ 1
## Positive: ZEB2, AFF3, AC105402.3, AOAH, VCAN, IGKC, RPL41, PLXDC2, HDAC9, CDK14
## IGHM, SETBP1, RPL13, UBE2E2, MTRNR2L8, RPLP2, GNLY, NKG7, CCL5, ACTB
## Negative: INPP4B, CAMK4, PAG1, SERINC5, CDC14A, CASK, ARHGAP15, ANK3, RORA, HIVEP2
## MDFIC, DOCK10, LEF1, KLF12, PRKCA, SKAP1, AKT3, GPRIN3, RASGRF2, MAML2
## PC_ 2
## Positive: TSHZ2, LEF1, FHIT, PLCL1, LTB, TTN, RPL13, SESN3, RPLP2, F5
## PRKCA, EEF1A1, RTKN2, MAP3K1, TXK, GCNT4, FAM13A, RPL41, TMSB10, LDLRAD4
## Negative: TGFBR3, C1orf21, AOAH, ZEB2, PPP2R2B, PLCB1, PDGFD, MYBL1, SYTL2, STAT4
## AGAP1, PARP8, NCALD, AC243829.2, THEMIS, DTHD1, GTDC1, A2M, PZP, LINC00299
## PC_ 3
## Positive: NELL2, ANK3, NR3C2, AC105402.3, RASGRF2, PRKCA, AC139720.1, PCSK5, BCL2, MTRNR2L8
## PRKN, SBF2, EDA, MAN1C1, IGF1R, SATB1-AS1, ADAM23, TXK, TAFA1, RNF157
## Negative: LINC02694, IKZF2, AC013652.1, TOX, AC093865.1, TTN, CDHR3, STAM, CCDC141, ST8SIA6
## RTKN2, DUSP4, MIR4435-2HG, TSHR, NIBAN1, HPGD, ATXN7L1, F5, MIR181A1HG, IL2RA
## PC_ 4
## Positive: PLXDC2, AFF3, VCAN, UBE2E2, HDAC9, CDK14, MTSS1, ZEB2, TCF7L2, AC105402.3
## CCSER1, MAML3, PDE4D, ALOX5, GAB2, CTBP2, FRY, VAV3, ZSWIM6, MAP3K1
## Negative: LINC01934, IFNG-AS1, ST8SIA1, ANK3, ITGA4, LRIG1, BICDL1, INPP4B, IL18RAP, THEMIS
## TPRG1, PCAT1, RASGRF2, GNAO1, SGPP2, RORA, FMN1, IL12RB2, SKAP1, MYBL1
## PC_ 5
## Positive: AL353660.1, GCNT4, ST8SIA1, TOX, AOAH, SESN3, RBMS3, TXK, LINC01934, C12orf42
## VAV3, SGPP2, TAFA2, KCNQ5, LEF1, MAML2, UBASH3B, IKZF2, SH3RF3, TRPS1
## Negative: FRY, ADAM12, LINC00299, RUNX2, PTPN13, ADAM19, CCR6, IL32, EEF1A1, PLD1
## LTB, B4GALT5, RPS19, LINC02694, AC013652.1, RPL13, PLCB1, MCF2L2, RBMS1, IL18R1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.3100 13.400 0.8680 88.70000 8.89e+01 93.0000
## 2 2 0.1290 3.850 0.7940 45.60000 4.56e+01 50.4000
## 3 3 0.0042 -0.428 0.7500 23.60000 2.34e+01 27.9000
## 4 4 0.1370 -2.000 0.6030 12.30000 1.21e+01 15.7000
## 5 5 0.3850 -2.840 0.7550 6.47000 6.27e+00 9.0400
## 6 6 0.6200 -3.200 0.7870 3.43000 3.26e+00 5.2700
## 7 7 0.8230 -3.510 0.8670 1.83000 1.71e+00 3.1200
## 8 8 0.8930 -3.640 0.9090 0.99000 9.13e-01 1.8700
## 9 9 0.8730 -3.510 0.8660 0.53900 4.91e-01 1.1300
## 10 10 0.8820 -3.230 0.8670 0.29700 2.62e-01 0.6930
## 11 12 0.8900 -2.870 0.8760 0.09260 7.93e-02 0.2670
## 12 14 0.9610 -2.350 0.9660 0.03020 2.37e-02 0.1060
## 13 16 0.9010 -2.070 0.8870 0.01030 7.27e-03 0.0430
## 14 18 0.2370 -3.530 0.0311 0.00373 2.33e-03 0.0208
## 15 20 0.3470 -5.610 0.1820 0.00142 7.79e-04 0.0120
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 121 21 13 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.
## $yellow
## [1] "INPP4B" "CAMK4" "PAG1" "SERINC5" "CDC14A"
## [6] "CASK" "ARHGAP15" "ANK3" "RORA" "HIVEP2"
## [11] "MDFIC" "DOCK10" "LEF1" "KLF12" "PRKCA"
## [16] "AKT3" "RASGRF2" "MAML2" "FAAH2" "PDE3B"
## [21] "SOS1" "SESN3" "TXK" "CMTM8" "NELL2"
## [26] "NR3C2" "AC139720.1" "BCL2" "MAN1C1" "TAFA1"
## [31] "RNF157" "DPP4" "GREM2" "ST8SIA1" "LRIG1"
## [36] "PCAT1" "AL353660.1" "AC233976.1" "ADAM19" "RBMS1"
## [41] "MB21D2"
##
## $blue
## [1] "TTN" "RTKN2" "STAM" "CCDC141" "LINC02694"
## [6] "IKZF2" "AC013652.1" "AC093865.1" "CDHR3" "ST8SIA6"
## [11] "DUSP4" "TSHR" "IL2RA"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "INPP4B" "CAMK4" "PAG1" "SERINC5" "CDC14A"
## [6] "CASK" "ARHGAP15" "ANK3" "RORA" "HIVEP2"
## [11] "MDFIC" "DOCK10" "LEF1" "KLF12" "PRKCA"
## [16] "AKT3" "RASGRF2" "MAML2" "FAAH2" "PDE3B"
## [21] "SOS1" "SESN3" "TXK" "CMTM8" "NELL2"
## [26] "NR3C2" "AC139720.1" "BCL2" "MAN1C1" "TAFA1"
## [31] "RNF157" "DPP4" "GREM2" "ST8SIA1" "LRIG1"
## [36] "PCAT1" "AL353660.1" "AC233976.1" "ADAM19" "RBMS1"
## [41] "MB21D2"
##
## $blue
## [1] "TTN" "RTKN2" "STAM" "CCDC141" "LINC02694"
## [6] "IKZF2" "AC013652.1" "AC093865.1" "CDHR3" "ST8SIA6"
## [11] "DUSP4" "TSHR" "IL2RA"
##
## [1] "Bup.Nalo_3"
## PC_ 1
## Positive: RPL13, RPL41, RPS18, RPLP2, TMSB10, RPS19, LTB, TTN, AC093865.1, IKZF2
## CCDC141, XIST, RTKN2, TRBC1, MTRNR2L8, JUN, ENTPD1, F5, TSHZ2, CDHR3
## Negative: PARP8, THEMIS, ANK3, ARHGAP15, RBMS1, RORA, PLCB1, NR3C2, CDC14A, LINC01619
## MBNL1, PPP3CA, INPP4B, CBLB, ZBTB20, RASGRF2, MYBL1, MCTP2, ANTXR2, FKBP5
## PC_ 2
## Positive: STAM, IKZF2, PLCL1, CCDC141, AC093865.1, TTN, CDHR3, LDLRAD4, LINC02694, TSHZ2
## IL2RA, GNAQ, TOX, ZC2HC1A, MCF2L2, PKIA, RTKN2, SNED1, ATXN7L1, F5
## Negative: PLCB1, ZEB2, AOAH, ARHGAP26, AC105402.3, IFNG-AS1, C1orf21, CCL5, MVB12B, IL18RAP
## A2M, AGAP1, MCTP2, GNLY, MYBL1, PZP, THEMIS, YES1, PPP2R2B, DTHD1
## PC_ 3
## Positive: ZEB2, LINC02694, ARHGAP26, NIBAN1, IKZF2, C1orf21, AC093865.1, MIR4435-2HG, SAMD3, TOX
## GNLY, PPP2R2B, TGFBR3, ST8SIA6, AOAH, NCALD, CCDC141, AC013652.1, PDGFD, DTHD1
## Negative: PRKCA, ANK3, INPP4B, TXK, AC139720.1, CMTM8, NELL2, LEF1, AC233976.1, SESN3
## PCSK5, AL353660.1, BCL2, RPL13, BACH2, FAAH2, LTB, RPLP2, ADAMTS17, TSHZ2
## PC_ 4
## Positive: XIST, ITGA4, CNOT6L, MCOLN2, STAT1, ST8SIA1, FMN1, SESN3, AP000787.1, ANK3
## PDE4B, ARHGAP15, LTB, HIVEP3, ESR1, IL12RB2, LINC01934, PHACTR2, SLC9A9, ASAP1
## Negative: AC105402.3, MTRNR2L8, SAMD12, AL589693.1, NR3C2, RUNX2, IL2RA, KANK1, AL136456.1, ADAM23
## LINC00278, PRKN, GREM2, SETD7, ZNF516, ADAM12, RNF157, SLC16A10, BANK1, IKZF2
## PC_ 5
## Positive: ADAM19, PAG1, LINC02694, KAT2B, ADAM12, NIBAN1, RORA, AC013652.1, FRY, LRIG1
## RUNX2, LINC00299, B4GALT5, MB21D2, CCR6, KIAA0825, CDC14A, SNED1, DPP4, PLD1
## Negative: LYN, BANK1, RALGPS2, CDK14, FCRL1, EBF1, HDAC9, OSBPL10, WDFY4, AFF3
## TRIO, PIK3AP1, RRM2, ARHGAP24, ZEB2, TCF4, USP6NL, PLXDC2, MEF2C, COBLL1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.044900 9.580 0.89100 90.50000 9.04e+01 94.6000
## 2 2 0.093900 7.590 0.71500 46.40000 4.63e+01 50.8000
## 3 3 0.171000 26.700 0.02710 24.00000 2.38e+01 27.5000
## 4 4 0.020000 1.570 0.77000 12.50000 1.23e+01 15.2000
## 5 5 0.000153 0.102 0.84600 6.60000 6.50e+00 8.5900
## 6 6 0.018500 -0.919 0.92900 3.51000 3.44e+00 4.9200
## 7 7 0.155000 -2.020 0.88900 1.89000 1.83e+00 2.8600
## 8 8 0.200000 -1.640 0.79400 1.03000 9.84e-01 1.6800
## 9 9 0.505000 -2.110 0.70300 0.57100 5.34e-01 1.0900
## 10 10 0.811000 -2.710 0.77500 0.32100 2.92e-01 0.7850
## 11 12 0.262000 -6.450 0.06270 0.10700 8.95e-02 0.4460
## 12 14 0.202000 -3.310 0.01270 0.03940 2.84e-02 0.2720
## 13 16 0.178000 -3.380 0.01330 0.01610 8.94e-03 0.1710
## 14 18 0.187000 -2.920 -0.00558 0.00730 2.90e-03 0.1100
## 15 20 0.021800 -1.040 0.07970 0.00366 9.74e-04 0.0708
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## [1] "No module detected"
## dynamicMods
## 0
## 179
## Error in hclust(as.dist(MEDiss), method = "average") :
## The distance structure is empty.
## [1] "Naltrexone_3"
## PC_ 1
## Positive: INPP4B, PAG1, PRKCA, ANK3, ARHGAP15, LEF1, CDC14A, MAP3K1, ADAM19, MGAT5
## BCL2, HIVEP2, TSHZ2, FAAH2, CASK, PLCL1, CMTM8, AC139720.1, SAMD12, BACH2
## Negative: ZEB2, C1orf21, AOAH, GNLY, SETBP1, OSBPL5, TGFBR3, ARHGAP26, LINC02384, AGAP1
## AC105402.3, PDGFD, MTRNR2L8, SYTL3, KLRD1, PPP2R2B, LYN, KLRK1, AC243829.2, MYO3B
## PC_ 2
## Positive: RPL13, RPLP2, RPS18, RPL13A, RPS28, RPLP1, RPL41, RPL28, RPS23, MTRNR2L8
## RPS19, RPS12, JUN, RPS2, FOS, LTB, FOSB, TSHZ2, JUNB, IER2
## Negative: PARP8, CBLB, ZEB2, MCTP2, C1orf21, MBNL1, TGFBR3, RORA, JAZF1, NCALD
## ARHGAP26, PPP3CA, MYBL1, CEMIP2, PPP2R2B, NIBAN1, LINC00278, PAM, PDGFD, LINC02384
## PC_ 3
## Positive: LINC02694, TTN, CCDC141, ENTPD1, IKZF2, RTKN2, STAM, AC093865.1, AC013652.1, TOX
## CDHR3, MIR181A1HG, IL2RA, HPGD, ZC2HC1A, F5, HACD1, BARD1, EZH2, DLEU2
## Negative: PLCB1, ANK3, NR3C2, RASGRF2, MYBL1, BACH2, THEMIS, PCSK5, BTBD11, NELL2
## ATP10A, TAFA1, RBMS1, SBF2, PELI2, IGF1R, EDA, PDE4D, DPP4, APBA2
## PC_ 4
## Positive: FOSB, FOS, JUN, RPS2, RPL13, RPLP2, RPS28, RPS12, RPLP1, RPL41
## RPL28, JUNB, RPS23, RPS19, RPS18, AC022217.3, LTB, RPL13A, IER2, EGR1
## Negative: FRY, PTPN13, AC105402.3, ADAM19, LINC00299, ADAM12, TANC1, MCF2L2, CCR6, LINC02649
## B4GALT5, AL589693.1, COL5A3, KIF5C, AFDN, FKBP5, AL136456.1, RORA, MYBL1, MTRNR2L8
## PC_ 5
## Positive: IKZF2, AC093865.1, TTN, ATXN7L1, CDHR3, ARID5B, LEF1, ST8SIA1, UBASH3B, RTKN2
## CCDC141, FCRL3, KLRC3, TOX, SESN3, AOAH, GCNT4, AL353660.1, LINC01727, APBA2
## Negative: RRM2, POLQ, NUSAP1, DIAPH3, MKI67, FAM111B, DTL, KIF18B, CENPU, SHCBP1
## TTK, CDC45, NCAPG, CLSPN, ANLN, SPC25, NCAPG2, E2F7, ASPM, ECT2
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.1490 13.900 0.56900 80.60000 80.50000 85.400
## 2 2 0.1770 7.670 0.58100 41.90000 42.00000 46.900
## 3 3 0.1250 4.130 0.67500 22.20000 22.10000 26.300
## 4 4 0.0133 0.879 0.83500 11.90000 11.80000 15.100
## 5 5 0.0130 -0.546 0.75800 6.49000 6.44000 8.760
## 6 6 0.3070 -2.450 0.94600 3.61000 3.55000 5.690
## 7 7 0.4430 -2.750 0.73600 2.04000 1.98000 3.830
## 8 8 0.6190 -2.690 0.76300 1.18000 1.12000 2.640
## 9 9 0.7300 -2.620 0.79700 0.69600 0.63700 1.860
## 10 10 0.7800 -2.430 0.74800 0.41900 0.36900 1.330
## 11 12 0.2950 -5.860 0.11500 0.16300 0.12800 0.708
## 12 14 0.2290 -4.320 0.01960 0.06920 0.04600 0.454
## 13 16 0.2200 -3.710 -0.00229 0.03230 0.01670 0.309
## 14 18 0.3250 -4.000 0.23400 0.01640 0.00626 0.218
## 15 20 0.3440 -4.700 0.16900 0.00908 0.00239 0.158
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7
## 70 15 14 13 13 12 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## $black
## [1] "INPP4B" "PAG1" "PRKCA" "ANK3" "ARHGAP15"
## [6] "LEF1" "CDC14A" "MAP3K1" "ADAM19" "MGAT5"
## [11] "BCL2" "HIVEP2" "TSHZ2" "FAAH2" "CASK"
## [16] "PLCL1" "CMTM8" "AC139720.1" "SAMD12" "ACVR1"
## [21] "TXK" "NR3C2" "MDFIC" "RASGRF2" "DPP4"
##
## $brown
## [1] "ZEB2" "C1orf21" "AOAH" "GNLY" "SETBP1"
## [6] "OSBPL5" "TGFBR3" "ARHGAP26" "LINC02384" "AGAP1"
## [11] "PDGFD" "SYTL3" "KLRD1" "PPP2R2B" "LYN"
## [16] "KLRK1" "AC243829.2" "PRSS23" "TMCC3" "MCTP2"
## [21] "SGCD" "NCALD" "MYBL1" "DNAJC1" "PLCB1"
##
## $blue
## [1] "RPL13" "RPLP2" "RPS18" "RPL13A" "RPS28"
## [6] "RPLP1" "RPL41" "RPL28" "RPS23" "RPS19"
## [11] "RPS12" "JUN" "RPS2" "FOS" "LTB"
## [16] "FOSB" "JUNB" "IER2" "AC022217.3" "EGR1"
## [21] "TEX14" "DNAJA1" "AC253572.2" "IFRD1" "EIF4A3"
##
## $yellow
## [1] "LINC02694" "TTN" "CCDC141" "ENTPD1" "IKZF2"
## [6] "RTKN2" "STAM" "AC093865.1" "AC013652.1" "IL2RA"
## [11] "HPGD" "ZC2HC1A" "HACD1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $black
## [1] "INPP4B" "PAG1" "PRKCA" "ANK3" "ARHGAP15"
## [6] "LEF1" "CDC14A" "MAP3K1" "ADAM19" "MGAT5"
## [11] "BCL2" "HIVEP2" "TSHZ2" "FAAH2" "CASK"
## [16] "PLCL1" "CMTM8" "AC139720.1" "SAMD12" "ACVR1"
## [21] "TXK" "NR3C2" "MDFIC" "RASGRF2" "DPP4"
##
## $brown
## [1] "ZEB2" "C1orf21" "AOAH" "GNLY" "SETBP1"
## [6] "OSBPL5" "TGFBR3" "ARHGAP26" "LINC02384" "AGAP1"
## [11] "PDGFD" "SYTL3" "KLRD1" "PPP2R2B" "LYN"
## [16] "KLRK1" "AC243829.2" "PRSS23" "TMCC3" "MCTP2"
## [21] "SGCD" "NCALD" "MYBL1" "DNAJC1" "PLCB1"
##
## $blue
## [1] "RPL13" "RPLP2" "RPS18" "RPL13A" "RPS28"
## [6] "RPLP1" "RPL41" "RPL28" "RPS23" "RPS19"
## [11] "RPS12" "JUN" "RPS2" "FOS" "LTB"
## [16] "FOSB" "JUNB" "IER2" "AC022217.3" "EGR1"
## [21] "TEX14" "DNAJA1" "AC253572.2" "IFRD1" "EIF4A3"
##
## $yellow
## [1] "LINC02694" "TTN" "CCDC141" "ENTPD1" "IKZF2"
## [6] "RTKN2" "STAM" "AC093865.1" "AC013652.1" "IL2RA"
## [11] "HPGD" "ZC2HC1A" "HACD1"
##
## [1] "Naltrexone_0"
## PC_ 1
## Positive: RPLP2, RPL13, MTRNR2L8, RPS23, RPL41, RPS18, RPS12, FOS, JUN, FOSB
## IER2, JUNB, AC022217.3, AL691403.1, EGR1, AC103591.3, CSKMT, SH3RF3, TTN, AFF3
## Negative: ARHGAP15, RORA, LINC01619, MBNL1, GPRIN3, SOS1, PAG1, PARP8, RABGAP1L, CDC14A
## FRY, RBMS1, INPP4B, RUNX2, MGAT5, PPP3CA, CBLB, ADAM19, THEMIS, ARL15
## PC_ 2
## Positive: INPP4B, PRKCA, ANK3, LEF1, PAG1, BCL2, TSHZ2, BACH2, MAML2, PLCL1
## CDC14A, XIST, CMTM8, NELL2, ARHGAP15, RPL13, MGAT5, FAAH2, FMN1, RPLP2
## Negative: ZEB2, C1orf21, AOAH, GNLY, SYNE1, SETBP1, LINC02384, AC243829.2, PDGFD, OSBPL5
## KLRD1, PRSS23, TGFBR3, SAMD3, KLRK1, LYN, ADGRG5, ARHGAP26, PPP2R2B, KLRC3
## PC_ 3
## Positive: LINC02694, STAM, ENTPD1, AC013652.1, TTN, MCF2L2, RTKN2, DUSP4, CCDC141, IL2RA
## NIBAN1, HPGD, ZC2HC1A, AC093865.1, PALM2-AKAP2, IKZF2, EZH2, MIR181A1HG, BARD1, KIF20B
## Negative: NELL2, IGF1R, RASGRF2, BACH2, NR3C2, PCSK5, PLCB1, AOAH, MCTP2, TAFA1
## C1orf21, RPL41, RPS23, PRKN, RPS12, SBF2, ANK3, RPL13, RPLP2, RPS18
## PC_ 4
## Positive: FRY, PDE4D, PTPN13, ADAM12, PLCB1, ADAM19, LINC00299, MYBL1, BTBD11, LATS2
## AL136456.1, RORA, CR1, MB21D2, ELOVL4, SOS1, AUTS2, CCR6, ALOX5, AL589693.1
## Negative: IKZF2, FOSB, LEF1, JUN, FOS, TOX, RPL41, AC093865.1, RPS23, AC022217.3
## TTN, MBNL1, CCDC141, RPS12, RPL13, RPLP2, RPS18, SESN3, PLCG2, JUNB
## PC_ 5
## Positive: UBASH3B, FAAH2, CMTM8, AL353660.1, TSHZ2, GRK5, AC139720.1, ST8SIA1, LEF1, FKBP5
## AK5, AC233976.1, IFNG-AS1, TMEM45B, DISC1, ATXN7L1, MAML2, SLC22A23, ADAMTS17, SORCS3
## Negative: JUN, FOSB, FOS, AC022217.3, DNAJA1, JUNB, IER2, RPL41, RPS12, RPS23
## ANXA1, AL691403.1, RPS18, RPLP2, RPL13, EGR1, AL606489.1, TEX14, NAMPT, PDE4D
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 2.02e-01 62.6000 0.07410 84.90000 84.60000 90.100
## 2 2 1.80e-01 28.8000 0.04210 43.80000 43.50000 49.600
## 3 3 1.65e-01 17.9000 0.01190 22.90000 22.60000 27.700
## 4 4 4.26e-03 0.5410 0.78400 12.00000 11.90000 15.700
## 5 5 7.62e-05 -0.0555 0.87800 6.43000 6.37000 8.980
## 6 6 6.37e-04 -0.1230 0.95300 3.47000 3.42000 5.230
## 7 7 6.17e-03 -0.2620 0.81900 1.90000 1.86000 3.080
## 8 8 1.26e-01 -1.0700 0.58700 1.06000 1.02000 1.970
## 9 9 2.69e-01 -1.4700 0.20000 0.60200 0.55700 1.300
## 10 10 5.48e-01 -1.8200 0.42700 0.34900 0.31100 0.939
## 11 12 7.71e-01 -1.9200 0.76200 0.12500 0.09770 0.558
## 12 14 4.35e-02 -1.4100 0.01180 0.05020 0.03200 0.356
## 13 16 6.83e-01 -1.3800 0.82100 0.02250 0.01120 0.235
## 14 18 1.00e-01 -1.6000 -0.00218 0.01120 0.00373 0.158
## 15 20 2.05e-01 -2.0100 -0.01970 0.00612 0.00129 0.107
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1
## 149 18
## Error in graphics:::plotHclust(n1, merge, height, order(x$order), hang, :
## invalid dendrogram input
## [1] "Methadone_3"
## PC_ 1
## Positive: RPL13, RPLP2, RPLP1, RPS18, RPS27, RPL41, RPS2, JUN, FOS, FOSB
## AC243829.2, C1orf21, NKG7, AC022217.3, GNLY, FMN1, CLNK, RBFOX3, LYN, EPDR1
## Negative: ARHGAP15, MBNL1, RORA, INPP4B, DPYD, ZBTB20, THEMIS, CDC14A, MDFIC, GPRIN3
## TNFAIP8, ANTXR2, HIVEP2, PLCG2, DOCK10, RABGAP1L, RBMS1, MGAT5, MAML2, PHACTR2
## PC_ 2
## Positive: ZEB2, GNLY, AOAH, SETBP1, KLRD1, AC243829.2, SAMD3, SYNE1, PDGFD, C1orf21
## KLRK1, TGFBR3, OSBPL5, ARHGAP26, LINC02384, PLEK, PPP2R2B, ADGRG5, VAV3, ATP8B4
## Negative: PRKCA, ANK3, LEF1, INPP4B, TSHZ2, BCL2, MGAT5, BACH2, NR3C2, NELL2
## FAAH2, CDC14A, CMTM8, RPL13, AC139720.1, GNAQ, RASGRF2, PCSK5, RPS18, HIVEP2
## PC_ 3
## Positive: LINC02694, ASPM, DIAPH3, NCAPG, MIR181A1HG, RRM2, AC013652.1, KNL1, KIF18B, MKI67
## BUB1B, TOP2A, TTN, KIF15, E2F7, CCDC141, CDCA2, STAM, BARD1, DEPDC1B
## Negative: ANK3, MCTP2, TAFA1, NR3C2, PLCB1, MYBL1, NELL2, KLRD1, AOAH, RASGRF2
## GNLY, ZEB2, ITGA4, SBF2, ATP10A, UST, SNTB1, OSBPL5, AC243829.2, RNF144A
## PC_ 4
## Positive: LINC02694, STAM, TTN, FANK1, AC013652.1, CCDC141, IKZF2, IL2RA, AC093865.1, CYTOR
## ATXN7L1, AL136456.1, CDHR3, MCF2L2, RTKN2, TOX, SNED1, HACD1, IL7, CTLA4
## Negative: DIAPH3, KIF18B, E2F7, CDCA2, KIF15, BUB1B, RRM2, KIFC1, ASPM, GTSE1
## DEPDC1B, MKI67, TOP2A, CDCA8, POLQ, CDC25C, CDK1, CENPI, ESPL1, ANLN
## PC_ 5
## Positive: FRY, LINC00299, PTPN13, MB21D2, LINC00511, RUNX2, THEMIS, AUTS2, TSPAN18, RORA
## MSC-AS1, AFDN, RBMS1, B4GALT5, MCF2L2, KIAA0825, ZNF462, PLCB1, HLF, TBXAS1
## Negative: IKZF2, VAV3, AC093865.1, RPLP2, RPL41, RPS2, RPLP1, TOX, SESN3, RPS18
## RPL13, RPS27, CCDC141, AL353660.1, SLC16A10, JUN, KCNQ5, PLCL1, TENM1, FOSB
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.015 -2.96 0.8800 93.2000 93.00000 98.200
## 2 2 0.214 -5.52 0.8410 48.5000 48.40000 54.500
## 3 3 0.418 -6.05 0.9450 25.6000 25.50000 31.400
## 4 4 0.390 -4.58 0.8750 13.7000 13.50000 18.800
## 5 5 0.552 -4.21 0.8500 7.4200 7.21000 11.800
## 6 6 0.685 -3.67 0.8200 4.1000 3.93000 7.730
## 7 7 0.758 -3.30 0.8330 2.3100 2.18000 5.270
## 8 8 0.877 -3.06 0.8890 1.3300 1.20000 3.720
## 9 9 0.916 -2.76 0.9030 0.7870 0.69100 2.700
## 10 10 0.918 -2.56 0.8960 0.4770 0.39500 2.000
## 11 12 0.921 -2.12 0.8990 0.1900 0.13400 1.160
## 12 14 0.260 -3.18 0.0646 0.0838 0.04550 0.694
## 13 16 0.253 -2.79 0.0641 0.0406 0.01630 0.426
## 14 18 0.246 -2.47 0.0574 0.0212 0.00590 0.265
## 15 20 0.240 -2.24 0.0528 0.0117 0.00216 0.167## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3 4
## 123 21 14 13 11## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $yellow
## [1] "RPL13" "RPLP2" "RPLP1" "RPS18" "RPS27"
## [6] "RPL41" "RPS2" "JUN" "FOS" "FOSB"
## [11] "AC022217.3"
##
## $turquoise
## [1] "AC243829.2" "C1orf21" "GNLY" "RBFOX3" "SGCD"
## [6] "AOAH" "ZEB2" "SETBP1" "KLRD1" "SAMD3"
## [11] "SYNE1" "PDGFD" "KLRK1" "TGFBR3" "OSBPL5"
## [16] "ARHGAP26" "LINC02384" "PLEK" "PPP2R2B" "FAM49A"
## [21] "DTHD1"
##
## $blue
## [1] "ASPM" "DIAPH3" "NCAPG" "RRM2" "KNL1" "KIF18B" "MKI67"
## [8] "BUB1B" "TOP2A" "KIF15" "E2F7" "CDCA2" "DEPDC1B" "MELK"
## [15] "GTSE1" "CENPU" "CDK1" "KIFC1" "CDCA8" "POLQ" "CDC25C"
## [22] "CENPI" "ESPL1" "ANLN" "PCLAF" "BRIP1" "BRCA2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "RPL13" "RPLP2" "RPLP1" "RPS18" "RPS27"
## [6] "RPL41" "RPS2" "JUN" "FOS" "FOSB"
## [11] "AC022217.3"
##
## $turquoise
## [1] "AC243829.2" "C1orf21" "GNLY" "RBFOX3" "SGCD"
## [6] "AOAH" "ZEB2" "SETBP1" "KLRD1" "SAMD3"
## [11] "SYNE1" "PDGFD" "KLRK1" "TGFBR3" "OSBPL5"
## [16] "ARHGAP26" "LINC02384" "PLEK" "PPP2R2B" "FAM49A"
## [21] "DTHD1"
##
## $blue
## [1] "ASPM" "DIAPH3" "NCAPG" "RRM2" "KNL1" "KIF18B" "MKI67"
## [8] "BUB1B" "TOP2A" "KIF15" "E2F7" "CDCA2" "DEPDC1B" "MELK"
## [15] "GTSE1" "CENPU" "CDK1" "KIFC1" "CDCA8" "POLQ" "CDC25C"
## [22] "CENPI" "ESPL1" "ANLN" "PCLAF" "BRIP1" "BRCA2"
##
## [1] "Methadone_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7423## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.2937e-16## PC_ 1
## Positive: ZEB2, AOAH, GNLY, AC243829.2, C1orf21, SETBP1, KLRD1, KLRK1, DTHD1, TGFBR3
## LINC02384, OSBPL5, SAMD3, TPST2, SGCD, PDGFD, SLC4A4, PPP2R2B, AL392086.3, LYN
## Negative: INPP4B, CAMK4, PRKCA, LEF1, ANK3, ARHGAP15, PAG1, MAP3K1, HIVEP2, MGAT5
## GNAQ, TSHZ2, ADAM19, FAAH2, MAML2, BCL2, CSGALNACT1, MDFIC, AC139720.1, GPRIN3
## PC_ 2
## Positive: CBLB, ZEB2, RABGAP1L, ARHGAP26, TGFBR3, STAT4, SAMD3, AOAH, PARP8, C1orf21
## JAZF1, MCTP2, AC243829.2, NCALD, CMIP, GNLY, SYTL2, PRKCB, PPP2R2B, PAM
## Negative: RPLP2, RPL41, TMSB10, FOS, JUN, AC022217.3, FOSB, MTRNR2L1, PLXNA4, TSHZ2
## AL691403.1, PRKCA, AC103591.3, IER2, AL109930.1, FHIT, LEF1-AS1, ERCC1, TULP2, EIF4A3
## PC_ 3
## Positive: LINC02694, TTN, RTKN2, CCDC141, IKZF2, AC013652.1, STAM, F5, IL2RA, CTLA4
## HPGD, AC093865.1, ENTPD1, TOX, BARD1, ST8SIA6, CDHR3, SLC16A10, PALM2-AKAP2, ZC2HC1A
## Negative: ANK3, NELL2, PITPNC1, RASGRF2, NR3C2, BACH2, ITGA4, PCSK5, THEMIS, MYBL1
## PLCB1, UST, SBF2, PELI2, IGF1R, PRKCB, PRKN, RBMS1, EDA, SATB1-AS1
## PC_ 4
## Positive: LINC00299, FRY, RUNX2, ADAM19, MB21D2, MYBL1, ADAM12, PTPN13, PDE4D, KAT2B
## MCF2L2, PLCB1, B4GALT5, AUTS2, NTN4, AL136456.1, MSC-AS1, SOS1, DENND3, SASH1
## Negative: AL353660.1, MAN2A1, ST8SIA1, BACH1, TOX, KCNQ5, MAML2, FHIT, LEF1, RPLP2
## UBASH3B, RPL41, CERS6, GCNT4, IKZF2, LRRC8D, SESN3, TMSB10, GLCCI1, TXK
## PC_ 5
## Positive: JUN, DTL, FOSB, FOS, POLQ, CCNE2, DIAPH3, NCAPG, RRM2, KIF15
## MKI67, SPC25, PCNA, WDR62, KIF11, ASPM, CENPU, POC1A, CIT, BUB1B
## Negative: CHST11, IL2RA, SLC9A9, ATXN7L1, ST8SIA1, CDHR3, TTN, UBASH3B, AHCYL2, TOX
## AF165147.1, JAZF1, SMAD3, LRIG1, GMDS-DT, PHACTR2, ARID5B, GNAO1, CNNM2, SAMD3
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.0786 -12.70 0.76100 1.24e+02 1.24e+02 129.000
## 2 2 0.1530 -8.62 0.83600 6.36e+01 6.36e+01 69.900
## 3 3 0.1250 -4.70 0.97000 3.30e+01 3.29e+01 38.200
## 4 4 0.1990 -4.07 0.87100 1.73e+01 1.72e+01 21.700
## 5 5 0.5640 -6.16 0.90500 9.16e+00 9.05e+00 13.200
## 6 6 0.6960 -5.37 0.84200 4.90e+00 4.78e+00 8.310
## 7 7 0.7780 -4.72 0.81300 2.66e+00 2.55e+00 5.430
## 8 8 0.8650 -4.31 0.84300 1.46e+00 1.37e+00 3.660
## 9 9 0.8980 -3.76 0.87000 8.16e-01 7.47e-01 2.530
## 10 10 0.2460 -5.01 0.04720 4.64e-01 4.10e-01 1.790
## 11 12 0.2570 -4.08 0.05940 1.59e-01 1.27e-01 0.938
## 12 14 0.3250 -5.75 0.13500 5.95e-02 4.00e-02 0.519
## 13 16 0.2200 -3.55 0.02760 2.45e-02 1.31e-02 0.298
## 14 18 0.2150 -3.14 0.01440 1.11e-02 4.33e-03 0.176
## 15 20 0.2070 -2.83 -0.00337 5.42e-03 1.47e-03 0.107## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3
## 206 15 12 10## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 3 module eigengenes in given set.## $brown
## [1] "ZEB2" "AOAH" "GNLY" "AC243829.2" "C1orf21"
## [6] "SETBP1" "KLRD1" "KLRK1" "DTHD1" "TGFBR3"
## [11] "LINC02384" "OSBPL5" "SAMD3" "TPST2" "SGCD"
## [16] "PDGFD" "SLC4A4" "AL392086.3" "LYN" "NCAM1"
## [21] "FAM49A" "LGR6" "JAZF1" "CEP78" "TRIO"
##
## $blue
## [1] "DTL" "POLQ" "CCNE2" "DIAPH3" "NCAPG" "RRM2" "KIF15" "MKI67"
## [9] "SPC25" "WDR62" "POC1A" "E2F7"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "6/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "ZEB2" "AOAH" "GNLY" "AC243829.2" "C1orf21"
## [6] "SETBP1" "KLRD1" "KLRK1" "DTHD1" "TGFBR3"
## [11] "LINC02384" "OSBPL5" "SAMD3" "TPST2" "SGCD"
## [16] "PDGFD" "SLC4A4" "AL392086.3" "LYN" "NCAM1"
## [21] "FAM49A" "LGR6" "JAZF1" "CEP78" "TRIO"
##
## $blue
## [1] "DTL" "POLQ" "CCNE2" "DIAPH3" "NCAPG" "RRM2" "KIF15" "MKI67"
## [9] "SPC25" "WDR62" "POC1A" "E2F7"saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Treatment_Timepoint.rds")
results.split<-SplitObject(results, "Treatment")
#reduced softpower iteratively until I got three modules
conds<-cbind(c(5,5,6),c(7,8,8))
mods2<-WrapGroupModID(results.split, "NA", conds)## [1] "Bup.Nalo"
## PC_ 1
## Positive: BANK1, ZEB2, AFF3, AOAH, VCAN, IGKC, SLC8A1, AC105402.3, PLXDC2, RPL41
## CDK14, HDAC9, IGHM, SETBP1, UBE2E2, RPL13, TRIO, MTRNR2L8, RPLP2, GNLY
## Negative: INPP4B, PAG1, CDC14A, ARHGAP15, SERINC5, ANK3, RORA, MDFIC, AKT3, PRKCA
## RASGRF2, PDE3B, LEF1, ZBTB20, MBNL1, MGAT5, MAML2, SOS1, RBMS1, NR3C2
## PC_ 2
## Positive: PLCB1, ARHGAP26, ZEB2, AOAH, THEMIS, MYBL1, STAT4, PARP8, C1orf21, TGFBR3
## IFNG-AS1, AGAP1, SYTL2, PPP2R2B, SBF2, A2M, IL18RAP, PZP, PDGFD, AUTS2
## Negative: TTN, IKZF2, STAM, TSHZ2, AC093865.1, CCDC141, RTKN2, LINC02694, PLCL1, CDHR3
## F5, AC013652.1, IL2RA, LDLRAD4, ZC2HC1A, LEF1, MCF2L2, FHIT, TAFA2, TOX
## PC_ 3
## Positive: LINC02694, TOX, IKZF2, NIBAN1, MIR4435-2HG, TGFBR3, AC013652.1, AC093865.1, PPP2R2B, ST8SIA6
## C1orf21, ARHGAP26, GTDC1, NCALD, CCDC141, HPGD, PAM, STAM, MSC-AS1, AF165147.1
## Negative: PRKCA, NELL2, AC139720.1, TXK, ANK3, MTRNR2L8, CMTM8, BACH2, SERINC5, PCSK5
## LEF1, AC233976.1, AC105402.3, NR3C2, RPL13, EDA, IGF1R, BCL2, PRKN, RPLP2
## PC_ 4
## Positive: TNFAIP3, IFNG-AS1, ANK3, IL18RAP, LRIG1, XIST, IL12RB2, FMN1, MCOLN2, IL32
## IL18R1, LINC01934, A2M, ITGA4, INPP4B, CNOT6L, LTB, FKBP5, RNF19A, AF165147.1
## Negative: BANK1, AFF3, SLC8A1, PLXDC2, GRK3, VCAN, UBE2E2, CDK14, HDAC9, MTSS1
## TRIO, BACH2, ZEB2, CCSER1, TCF7L2, MAML3, CTBP2, IGHM, ALOX5, TCF4
## PC_ 5
## Positive: ST8SIA1, ITGA4, SESN3, LINC01934, AL353660.1, TOX, AOAH, APBA2, TRPS1, TXK
## C12orf42, GCNT4, LEF1, MAML2, SGPP2, CERS6, LRRC8D, KCNQ5, SLC9A9, DTHD1
## Negative: ADAM12, FRY, RUNX2, CCR6, LINC00299, PTPN13, PLCB1, PLD1, AL136456.1, MTRNR2L8
## AC105402.3, LINC02694, B4GALT5, MB21D2, AL589693.1, RBMS1, PDE4D, ADAM23, CFH, AC013652.1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00922 3.310 0.9520 84.40000 8.44e+01 88.4000
## 2 2 0.02700 3.110 0.9570 43.30000 4.31e+01 47.7000
## 3 3 0.00795 1.120 0.8960 22.40000 2.22e+01 26.0000
## 4 4 0.00748 -0.913 0.7570 11.70000 1.15e+01 14.4000
## 5 5 0.01410 -0.915 0.7810 6.13000 6.02e+00 8.0800
## 6 6 0.05210 -1.560 0.6150 3.25000 3.16e+00 4.6500
## 7 7 0.28100 -3.150 0.4940 1.74000 1.69e+00 2.7100
## 8 8 0.64200 -3.690 0.7450 0.94200 8.97e-01 1.6000
## 9 9 0.81200 -3.760 0.8580 0.51500 4.91e-01 0.9580
## 10 10 0.91100 -3.620 0.9210 0.28400 2.67e-01 0.5790
## 11 12 0.85800 -2.840 0.8300 0.08990 8.06e-02 0.2180
## 12 14 0.87100 -2.240 0.8360 0.03000 2.55e-02 0.0927
## 13 16 0.90900 -2.090 0.8850 0.01060 8.37e-03 0.0472
## 14 18 0.24700 -3.550 0.0388 0.00401 2.77e-03 0.0267
## 15 20 0.32000 -4.480 0.1960 0.00163 9.11e-04 0.0159## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3 4
## 112 17 14 14 10## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $blue
## [1] "BANK1" "AFF3" "VCAN" "IGKC" "SLC8A1" "PLXDC2" "CDK14" "HDAC9"
## [9] "IGHM" "SETBP1" "UBE2E2" "TRIO" "GRK3" "TCF4"
##
## $yellow
## [1] "ZEB2" "AOAH" "ARHGAP26" "C1orf21" "TGFBR3"
## [6] "AGAP1" "PPP2R2B" "PDGFD" "DTHD1" "AC243829.2"
##
## $turquoise
## [1] "INPP4B" "PAG1" "CDC14A" "ARHGAP15" "SERINC5"
## [6] "ANK3" "MDFIC" "PRKCA" "RASGRF2" "PDE3B"
## [11] "MGAT5" "MAML2" "NR3C2" "AC139720.1" "NELL2"
## [16] "BCL2" "PRKN"
##
## $brown
## [1] "TTN" "IKZF2" "STAM" "AC093865.1" "CCDC141"
## [6] "RTKN2" "LINC02694" "CDHR3" "AC013652.1" "IL2RA"
## [11] "TOX" "ATXN7L1" "ST8SIA6" "HPGD"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "BANK1" "AFF3" "VCAN" "IGKC" "SLC8A1" "PLXDC2" "CDK14" "HDAC9"
## [9] "IGHM" "SETBP1" "UBE2E2" "TRIO" "GRK3" "TCF4"
##
## $yellow
## [1] "ZEB2" "AOAH" "ARHGAP26" "C1orf21" "TGFBR3"
## [6] "AGAP1" "PPP2R2B" "PDGFD" "DTHD1" "AC243829.2"
##
## $turquoise
## [1] "INPP4B" "PAG1" "CDC14A" "ARHGAP15" "SERINC5"
## [6] "ANK3" "MDFIC" "PRKCA" "RASGRF2" "PDE3B"
## [11] "MGAT5" "MAML2" "NR3C2" "AC139720.1" "NELL2"
## [16] "BCL2" "PRKN"
##
## $brown
## [1] "TTN" "IKZF2" "STAM" "AC093865.1" "CCDC141"
## [6] "RTKN2" "LINC02694" "CDHR3" "AC013652.1" "IL2RA"
## [11] "TOX" "ATXN7L1" "ST8SIA6" "HPGD"
##
## [1] "Naltrexone"
## PC_ 1
## Positive: INPP4B, PRKCA, LEF1, ANK3, TSHZ2, PAG1, BCL2, CMTM8, PLCL1, CDC14A
## RPL13, BACH2, XIST, FAAH2, RPLP2, NELL2, RPS18, MAP3K1, AC139720.1, AL589693.1
## Negative: ZEB2, C1orf21, AOAH, SYNE1, GNLY, SETBP1, TGFBR3, LINC02384, SAMD3, OSBPL5
## PDGFD, ARHGAP26, PPP2R2B, KLRD1, AGAP1, ADGRG5, AC243829.2, KLRK1, LYN, SYTL3
## PC_ 2
## Positive: MTRNR2L8, RPL13, RPLP2, RPLP1, RPL41, RPS18, RPS28, RPS23, RPS19, RPS12
## RPS2, FOS, JUN, FOSB, JUNB, IER2, AC022217.3, AL691403.1, EGR1, AC105402.3
## Negative: ARHGAP15, RORA, MBNL1, PAG1, CDC14A, INPP4B, MGAT5, RBMS1, MDFIC, PARP8
## RABGAP1L, FRY, RUNX2, ADAM19, PPP3CA, THEMIS, MAP3K1, ANK3, CBLB, SMYD3
## PC_ 3
## Positive: LINC02694, TTN, ENTPD1, CCDC141, STAM, AC013652.1, RTKN2, IL2RA, IKZF2, AC093865.1
## DUSP4, HPGD, NIBAN1, TOX, MCF2L2, ZC2HC1A, PALM2-AKAP2, F5, MIR181A1HG, CDHR3
## Negative: BACH2, NELL2, RASGRF2, PLCB1, IGF1R, NR3C2, RPL41, PCSK5, RPS2, RPS12
## RPS23, RPL13, RPLP2, ANK3, RPS19, RPS18, RPS28, TAFA1, RPLP1, SBF2
## PC_ 4
## Positive: FRY, PTPN13, ADAM19, ADAM12, PDE4D, PLCB1, BTBD11, MYBL1, LINC00299, MB21D2
## ALOX5, RORA, AC105402.3, TANC1, AL589693.1, BCL2, MTRNR2L8, AL136456.1, PTPRM, AUTS2
## Negative: RPS2, FOSB, RPS28, RPL41, RPS23, JUN, FOS, RPLP1, RPS12, RPLP2
## RPS19, RPL13, RPS18, JUNB, AC022217.3, IKZF2, IER2, AC093865.1, PLCG2, DNAJA1
## PC_ 5
## Positive: JUN, PDE4D, FOSB, FOS, DNAJA1, ADAM12, JUNB, FRY, AC022217.3, LINC00299
## RPL41, RPS19, RPS2, IER2, RPS12, AL136456.1, RPLP1, RPS28, RPS23, NAMPT
## Negative: UBASH3B, LEF1, AL353660.1, ST8SIA1, AC139720.1, TSHZ2, SESN3, AC233976.1, CMTM8, GCNT4
## ATXN7L1, FAAH2, GRK5, IFNG-AS1, MAML2, CERS6, FHIT, AOAH, SLC9A9, FMN1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.187000 58.600 0.05800 79.9000 79.60000 84.700
## 2 2 0.174000 28.100 0.03250 41.4000 41.30000 46.700
## 3 3 0.054100 2.730 0.64000 21.8000 21.60000 26.200
## 4 4 0.003750 0.525 0.78200 11.6000 11.50000 14.900
## 5 5 0.000215 -0.084 0.73000 6.2800 6.19000 8.590
## 6 6 0.134000 -1.480 0.59800 3.4700 3.37000 5.260
## 7 7 0.446000 -2.320 0.66400 1.9500 1.86000 3.480
## 8 8 0.531000 -2.130 0.46200 1.1200 1.03000 2.360
## 9 9 0.575000 -2.250 0.46200 0.6600 0.57300 1.640
## 10 10 0.630000 -1.880 0.60800 0.3980 0.32300 1.210
## 11 12 0.064900 -2.020 -0.00604 0.1570 0.10700 0.711
## 12 14 0.031000 -1.540 0.14200 0.0694 0.03620 0.438
## 13 16 0.037900 -1.140 0.03000 0.0338 0.01250 0.276
## 14 18 0.043800 -1.100 0.01880 0.0178 0.00441 0.176
## 15 20 0.655000 -1.040 0.76800 0.0100 0.00168 0.113## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3
## 102 23 22 10## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $brown
## [1] "INPP4B" "PRKCA" "ANK3" "PAG1" "BCL2" "CDC14A"
## [7] "MAP3K1" "ARHGAP15" "ADAM19" "ETV6"
##
## $blue
## [1] "RPL13" "RPLP2" "RPS18" "RPLP1" "RPS23"
## [6] "RPL41" "RPS28" "RPS19" "RPS12" "RPS2"
## [11] "FOS" "JUN" "FOSB" "JUNB" "IER2"
## [16] "AC022217.3" "AL691403.1" "EGR1" "EIF4A3" "TEX14"
## [21] "CSKMT" "DNAJA1"
##
## $turquoise
## [1] "ZEB2" "C1orf21" "AOAH" "SYNE1" "GNLY"
## [6] "SETBP1" "TGFBR3" "LINC02384" "SAMD3" "OSBPL5"
## [11] "PDGFD" "ARHGAP26" "PPP2R2B" "KLRD1" "AGAP1"
## [16] "ADGRG5" "AC243829.2" "KLRK1" "LYN" "SYTL3"
## [21] "PRSS23" "MCTP2" "VAV3"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "INPP4B" "PRKCA" "ANK3" "PAG1" "BCL2" "CDC14A"
## [7] "MAP3K1" "ARHGAP15" "ADAM19" "ETV6"
##
## $blue
## [1] "RPL13" "RPLP2" "RPS18" "RPLP1" "RPS23"
## [6] "RPL41" "RPS28" "RPS19" "RPS12" "RPS2"
## [11] "FOS" "JUN" "FOSB" "JUNB" "IER2"
## [16] "AC022217.3" "AL691403.1" "EGR1" "EIF4A3" "TEX14"
## [21] "CSKMT" "DNAJA1"
##
## $turquoise
## [1] "ZEB2" "C1orf21" "AOAH" "SYNE1" "GNLY"
## [6] "SETBP1" "TGFBR3" "LINC02384" "SAMD3" "OSBPL5"
## [11] "PDGFD" "ARHGAP26" "PPP2R2B" "KLRD1" "AGAP1"
## [16] "ADGRG5" "AC243829.2" "KLRK1" "LYN" "SYTL3"
## [21] "PRSS23" "MCTP2" "VAV3"
##
## [1] "Methadone"
## PC_ 1
## Positive: INPP4B, CAMK4, PRKCA, ANK3, LEF1, ARHGAP15, CDC14A, MGAT5, HIVEP2, GNAQ
## TSHZ2, NR3C2, FAAH2, BCL2, MAML2, AC139720.1, NELL2, PDE3B, BACH2, DOCK10
## Negative: ZEB2, AOAH, GNLY, AC243829.2, C1orf21, SETBP1, KLRD1, KLRK1, SYNE1, OSBPL5
## PDGFD, LINC02384, DTHD1, LYN, TGFBR3, SAMD3, ADGRG5, SGCD, SLC4A4, AL392086.3
## PC_ 2
## Positive: RPLP2, RPL41, RPS27, RPS2, FOS, JUN, FOSB, AC022217.3, TUBA1A, PLXNA4
## IER2, CLNK, FHIT, TSHZ2, SH3RF3, PRKCA, AL589693.1, EGR1, FMN1, SDK2
## Negative: RABGAP1L, SAMD3, MBNL1, TGFBR3, CBLB, ZEB2, JAZF1, ARHGAP15, PAM, ARHGAP26
## RORA, DPYD, NCALD, MCTP2, SYNE1, AOAH, GTDC1, DLEU2, ST8SIA4, PPP2R2B
## PC_ 3
## Positive: ANK3, NR3C2, NELL2, MYBL1, PLCB1, RASGRF2, MCTP2, TAFA1, ITGA4, BACH2
## SBF2, AOAH, UST, PCSK5, PELI2, ZEB2, PRKN, KLRD1, GNLY, KLRK1
## Negative: LINC02694, TTN, AC013652.1, CCDC141, STAM, MIR181A1HG, DIAPH3, NCAPG, ASPM, BARD1
## KNL1, IKZF2, RTKN2, MKI67, DUSP4, TOP2A, RRM2, F5, BUB1B, KIF15
## PC_ 4
## Positive: LINC02694, STAM, TTN, IKZF2, CCDC141, IL2RA, AC093865.1, AC013652.1, FANK1, CDHR3
## TOX, ATXN7L1, HACD1, RTKN2, CTLA4, IL7, SNED1, HPGD, MCF2L2, F5
## Negative: DIAPH3, KIF15, RRM2, BUB1B, ASPM, E2F7, POLQ, KIF18B, CDCA2, MKI67
## DEPDC1B, DTL, KIFC1, NCAPG, CDC25C, ANLN, TOP2A, PCLAF, CENPU, SPC25
## PC_ 5
## Positive: AL353660.1, TXK, IKZF2, KCNQ5, TOX, AC093865.1, SESN3, GCNT4, LEF1, BACH1
## CERS6, VAV3, UBASH3B, ST8SIA1, AC233976.1, ATXN7L1, FHIT, GLCCI1, MAML2, CDHR3
## Negative: FRY, LINC00299, PTPN13, RUNX2, MB21D2, ADAM12, AUTS2, PLCB1, MSC-AS1, RBMS1
## PDE4D, B4GALT5, MCF2L2, RORA, MYBL1, AFDN, PLD1, SASH1, HLF, SYTL2
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.113 -17.00 0.6740 1.10e+02 1.09e+02 115.0000
## 2 2 0.172 -8.89 0.7740 5.65e+01 5.63e+01 62.5000
## 3 3 0.194 -6.16 0.8820 2.94e+01 2.93e+01 34.5000
## 4 4 0.124 -3.41 0.9400 1.55e+01 1.53e+01 19.2000
## 5 5 0.119 -2.25 0.7460 8.21e+00 8.09e+00 10.9000
## 6 6 0.339 -3.06 0.7980 4.41e+00 4.33e+00 6.6900
## 7 7 0.603 -3.93 0.7860 2.40e+00 2.33e+00 4.3100
## 8 8 0.781 -3.69 0.8860 1.33e+00 1.25e+00 2.8600
## 9 9 0.191 -5.53 -0.0315 7.48e-01 6.78e-01 1.9500
## 10 10 0.209 -4.93 -0.0108 4.28e-01 3.75e-01 1.3600
## 11 12 0.326 -6.47 0.1450 1.49e-01 1.15e-01 0.6930
## 12 14 0.317 -6.04 0.1220 5.65e-02 3.54e-02 0.3690
## 13 16 0.267 -4.19 0.0642 2.33e-02 1.18e-02 0.2020
## 14 18 0.260 -3.71 0.0629 1.04e-02 3.98e-03 0.1130
## 15 20 0.314 -4.31 0.1590 4.98e-03 1.38e-03 0.0645## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3 4
## 150 27 13 13 12## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $blue
## [1] "INPP4B" "CAMK4" "PRKCA" "ANK3" "LEF1" "MGAT5" "HIVEP2"
## [8] "NR3C2" "MAML2" "NELL2" "PDE3B" "BACH2" "RASGRF2"
##
## $turquoise
## [1] "ZEB2" "AOAH" "GNLY" "AC243829.2" "C1orf21"
## [6] "SETBP1" "KLRD1" "KLRK1" "SYNE1" "OSBPL5"
## [11] "PDGFD" "LINC02384" "DTHD1" "LYN" "TGFBR3"
## [16] "SAMD3" "ADGRG5" "SGCD" "SLC4A4" "AL392086.3"
## [21] "ARHGAP26" "NCAM1" "PPP2R2B" "KLRF1" "FAM49A"
## [26] "JAZF1" "MCTP2"
##
## $brown
## [1] "DIAPH3" "NCAPG" "ASPM" "MKI67" "TOP2A" "RRM2" "BUB1B"
## [8] "KIF15" "CDCA2" "E2F7" "POLQ" "KIF18B" "DEPDC1B" "DTL"
## [15] "KIFC1" "CDC25C" "ANLN" "PCLAF" "CENPU" "SPC25" "PBK"
## [22] "ECT2" "POC1A" "CIT" "CDK1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "INPP4B" "CAMK4" "PRKCA" "ANK3" "LEF1" "MGAT5" "HIVEP2"
## [8] "NR3C2" "MAML2" "NELL2" "PDE3B" "BACH2" "RASGRF2"
##
## $turquoise
## [1] "ZEB2" "AOAH" "GNLY" "AC243829.2" "C1orf21"
## [6] "SETBP1" "KLRD1" "KLRK1" "SYNE1" "OSBPL5"
## [11] "PDGFD" "LINC02384" "DTHD1" "LYN" "TGFBR3"
## [16] "SAMD3" "ADGRG5" "SGCD" "SLC4A4" "AL392086.3"
## [21] "ARHGAP26" "NCAM1" "PPP2R2B" "KLRF1" "FAM49A"
## [26] "JAZF1" "MCTP2"
##
## $brown
## [1] "DIAPH3" "NCAPG" "ASPM" "MKI67" "TOP2A" "RRM2" "BUB1B"
## [8] "KIF15" "CDCA2" "E2F7" "POLQ" "KIF18B" "DEPDC1B" "DTL"
## [15] "KIFC1" "CDC25C" "ANLN" "PCLAF" "CENPU" "SPC25" "PBK"
## [22] "ECT2" "POC1A" "CIT" "CDK1"saveRDS(mods2, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Treatment.rds")
#reduced softpower iteratively until I got three modules
mods3<-ModID(results, nPCS = 8, softpower = 7)## PC_ 1
## Positive: ZEB2, AOAH, LYN, BANK1, GNLY, SETBP1, C1orf21, AC105402.3, AFF3, AC243829.2
## MTRNR2L8, CCL5, VCAN, KLRD1, EBF1, IGKC, SLC8A1, KLRK1, HDAC9, PDGFD
## Negative: INPP4B, PAG1, ARHGAP15, CDC14A, ANK3, PRKCA, LEF1, RORA, MGAT5, GPRIN3
## MDFIC, BCL2, ADAM19, MAP3K1, GNAQ, MAML2, RBMS1, MBNL1, NR3C2, PDE3B
## PC_ 2
## Positive: ZEB2, C1orf21, TGFBR3, ARHGAP26, PPP2R2B, MCTP2, AOAH, NCALD, PARP8, SYTL2
## LINC02384, PDGFD, MYBL1, AGAP1, GNLY, AC243829.2, MVB12B, PLCB1, KLRD1, OSBPL5
## Negative: RPL13, RPLP2, RPL41, TSHZ2, LEF1, PRKCA, JUNB, CMTM8, FHIT, FOS
## JUN, PLCL1, MTRNR2L8, SESN3, FOSB, TXK, AL109930.1, XIST, AC233976.1, AL353660.1
## PC_ 3
## Positive: ANK3, BACH2, NELL2, NR3C2, RASGRF2, PLCB1, SBF2, PCSK5, PELI2, PRKN
## THEMIS, IGF1R, TAFA1, MYBL1, RBMS1, UST, DPP4, PRKCA, EDA, BTBD11
## Negative: LINC02694, IKZF2, TTN, AC093865.1, CCDC141, STAM, AC013652.1, TOX, RTKN2, CDHR3
## DUSP4, IL2RA, F5, HPGD, MIR181A1HG, ZC2HC1A, ATXN7L1, ST8SIA6, ENTPD1, NIBAN1
## PC_ 4
## Positive: RORA, MYBL1, IL18RAP, SYTL2, TNFAIP3, LINC00299, TGFBR3, AGAP1, PPP2R2B, THEMIS
## HIVEP3, MCOLN2, LRIG1, NCALD, PTPRM, TPRG1, ANK3, C1orf21, NIBAN1, AGPAT4
## Negative: BANK1, AFF3, LYN, SLC8A1, PLXDC2, VCAN, GRK3, EBF1, UBE2E2, CDK14
## HDAC9, TRIO, IGKC, IGHM, BACH2, CCSER1, TCF4, MTSS1, EVI5, SOX5
## PC_ 5
## Positive: FRY, ADAM12, PDE4D, PTPN13, LINC00299, ADAM19, RUNX2, CCR6, PLCB1, MB21D2
## AL136456.1, MCF2L2, AUTS2, B4GALT5, GAB2, RBMS1, AFDN, ELOVL4, SOS1, AL589693.1
## Negative: AL353660.1, LEF1, ST8SIA1, SESN3, TXK, GCNT4, TOX, LINC01934, MAML2, MLLT3
## UBASH3B, AC233976.1, ATXN7L1, AC243829.2, IKZF2, AOAH, ITGA4, FHIT, AC093865.1, GLCCI1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.06620 15.800 0.6980 1.20e+02 1.20e+02 125.0000
## 2 2 0.02950 5.240 0.6450 6.14e+01 6.12e+01 67.0000
## 3 3 0.00232 0.932 0.7240 3.15e+01 3.13e+01 36.2000
## 4 4 0.00012 -0.154 0.7550 1.63e+01 1.61e+01 19.8000
## 5 5 0.00433 -0.726 0.6530 8.46e+00 8.34e+00 10.9000
## 6 6 0.02980 -1.530 0.6920 4.43e+00 4.34e+00 6.1100
## 7 7 0.04440 -1.470 0.6740 2.33e+00 2.27e+00 3.4600
## 8 8 0.15200 -8.450 0.1180 1.24e+00 1.19e+00 2.0200
## 9 9 0.58000 -3.770 0.7500 6.65e-01 6.34e-01 1.2300
## 10 10 0.25500 -8.520 0.0431 3.61e-01 3.37e-01 0.7680
## 11 12 0.34500 -7.550 0.2160 1.10e-01 9.92e-02 0.3120
## 12 14 0.33600 -5.830 0.2060 3.52e-02 2.95e-02 0.1340
## 13 16 0.30500 -4.570 0.1590 1.21e-02 8.83e-03 0.0599
## 14 18 0.79000 -1.820 0.7950 4.46e-03 2.80e-03 0.0278
## 15 20 0.82600 -1.590 0.8420 1.79e-03 9.09e-04 0.0158## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.## dynamicMods
## 0 1 2 3 4
## 188 14 14 11 11## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $blue
## [1] "LYN" "BANK1" "AFF3" "VCAN" "EBF1" "IGKC" "SLC8A1" "HDAC9"
## [9] "PLXDC2" "CDK14" "IGHM" "GRK3" "UBE2E2" "TRIO"
##
## $turquoise
## [1] "INPP4B" "PAG1" "ARHGAP15" "CDC14A" "ANK3"
## [6] "PRKCA" "LEF1" "MDFIC" "BCL2" "MAML2"
## [11] "NR3C2" "RASGRF2" "AC139720.1" "NELL2"
##
## $brown
## [1] "LINC02694" "IKZF2" "TTN" "AC093865.1" "CCDC141"
## [6] "STAM" "AC013652.1" "RTKN2" "IL2RA" "HPGD"
## [11] "FANK1"
##
## $yellow
## [1] "TOP2A" "MKI67" "ASPM" "NCAPG" "KIF15" "CENPF" "ANLN" "KIF18B"
## [9] "DLGAP5" "CDCA2" "KIF14"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "11/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "LYN" "BANK1" "AFF3" "VCAN" "EBF1" "IGKC" "SLC8A1" "HDAC9"
## [9] "PLXDC2" "CDK14" "IGHM" "GRK3" "UBE2E2" "TRIO"
##
## $turquoise
## [1] "INPP4B" "PAG1" "ARHGAP15" "CDC14A" "ANK3"
## [6] "PRKCA" "LEF1" "MDFIC" "BCL2" "MAML2"
## [11] "NR3C2" "RASGRF2" "AC139720.1" "NELL2"
##
## $brown
## [1] "LINC02694" "IKZF2" "TTN" "AC093865.1" "CCDC141"
## [6] "STAM" "AC013652.1" "RTKN2" "IL2RA" "HPGD"
## [11] "FANK1"
##
## $yellow
## [1] "TOP2A" "MKI67" "ASPM" "NCAPG" "KIF15" "CENPF" "ANLN" "KIF18B"
## [9] "DLGAP5" "CDCA2" "KIF14"saveRDS(mods3, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules.rds")devtools::session_info()## Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
## had status 1## - Session info ---------------------------------------------------------------
## setting value
## version R version 4.2.0 (2022-04-22)
## os Red Hat Enterprise Linux 8.7 (Ootpa)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate C
## ctype C
## tz Etc/UTC
## date 2023-06-01
## pandoc 2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
##
## - Packages -------------------------------------------------------------------
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [2] CRAN (R 4.2.0)
## AnnotationDbi 1.60.2 2023-03-10 [1] Bioconductor
## backports 1.4.1 2021-12-13 [2] CRAN (R 4.2.0)
## base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.2.0)
## Biobase 2.58.0 2022-11-01 [1] Bioconductor
## BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor
## BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
## Biostrings 2.66.0 2022-11-01 [1] Bioconductor
## bit 4.0.5 2022-11-15 [2] CRAN (R 4.2.0)
## bit64 4.0.5 2020-08-30 [2] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [2] CRAN (R 4.2.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.2.0)
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.2.0)
## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
## checkmate 2.1.0 2022-04-21 [2] CRAN (R 4.2.0)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.2.0)
## cluster 2.1.4 2022-08-22 [2] CRAN (R 4.2.0)
## codetools 0.2-19 2023-02-01 [2] CRAN (R 4.2.0)
## colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.2.0)
## cowplot * 1.1.1 2020-12-30 [2] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [2] CRAN (R 4.2.0)
## data.table 1.14.8 2023-02-17 [2] CRAN (R 4.2.0)
## DBI 1.1.3 2022-06-18 [2] CRAN (R 4.2.0)
## deldir 1.0-6 2021-10-23 [2] CRAN (R 4.2.0)
## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
## digest 0.6.31 2022-12-11 [2] CRAN (R 4.2.0)
## doParallel * 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
## dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.2.0)
## dynamicTreeCut * 1.63-1 2016-03-11 [2] CRAN (R 4.2.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.2.0)
## evaluate 0.20 2023-01-17 [2] CRAN (R 4.2.0)
## fansi 1.0.4 2023-01-22 [2] CRAN (R 4.2.0)
## fastcluster * 1.2.3 2021-05-24 [2] CRAN (R 4.2.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
## fastmatch 1.1-3 2021-07-23 [2] CRAN (R 4.2.0)
## fitdistrplus 1.1-8 2022-03-10 [2] CRAN (R 4.2.0)
## flashClust * 1.01-2 2012-08-21 [1] CRAN (R 4.2.0)
## foreach * 1.5.2 2022-02-02 [2] CRAN (R 4.2.0)
## foreign 0.8-84 2022-12-06 [2] CRAN (R 4.2.0)
## Formula 1.2-5 2023-02-24 [1] CRAN (R 4.2.0)
## fs 1.6.1 2023-02-06 [2] CRAN (R 4.2.0)
## future 1.32.0 2023-03-07 [1] CRAN (R 4.2.0)
## future.apply 1.10.0 2022-11-05 [1] CRAN (R 4.2.0)
## generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.0)
## GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor
## GenomeInfoDbData 1.2.9 2023-03-17 [1] Bioconductor
## GenomicRanges 1.50.2 2022-12-16 [1] Bioconductor
## ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.2.0)
## ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.2.0)
## ggridges 0.5.4 2022-09-26 [1] CRAN (R 4.2.0)
## globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.0)
## glue 1.6.2 2022-02-24 [2] CRAN (R 4.2.0)
## GO.db 3.16.0 2023-03-17 [1] Bioconductor
## goftest 1.2-3 2021-10-07 [2] CRAN (R 4.2.0)
## gridExtra 2.3 2017-09-09 [2] CRAN (R 4.2.0)
## gtable 0.3.3 2023-03-21 [1] CRAN (R 4.2.0)
## highr 0.10 2022-12-22 [1] CRAN (R 4.2.0)
## Hmisc * 5.1-0 2023-05-08 [1] CRAN (R 4.2.0)
## htmlTable 2.4.1 2022-07-07 [1] CRAN (R 4.2.0)
## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.2.0)
## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.2.0)
## httpuv 1.6.9 2023-02-14 [1] CRAN (R 4.2.0)
## httr 1.4.5 2023-02-24 [1] CRAN (R 4.2.0)
## ica 1.0-3 2022-07-08 [2] CRAN (R 4.2.0)
## igraph 1.4.2 2023-04-07 [1] CRAN (R 4.2.0)
## impute 1.72.3 2023-01-19 [1] Bioconductor
## IRanges 2.32.0 2022-11-01 [1] Bioconductor
## irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0)
## iterators * 1.0.14 2022-02-05 [2] CRAN (R 4.2.0)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.2.0)
## jsonlite 1.8.4 2022-12-06 [2] CRAN (R 4.2.0)
## KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
## KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.0)
## knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [2] CRAN (R 4.2.0)
## lattice 0.21-8 2023-04-05 [1] CRAN (R 4.2.0)
## lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.2.0)
## leiden 0.4.3 2022-09-10 [1] CRAN (R 4.2.0)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
## listenv 0.9.0 2022-12-16 [2] CRAN (R 4.2.0)
## lmtest 0.9-40 2022-03-21 [2] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.0)
## MASS 7.3-59 2023-04-21 [1] CRAN (R 4.2.0)
## Matrix 1.5-4 2023-04-04 [1] CRAN (R 4.2.0)
## matrixStats 0.63.0 2022-11-18 [2] CRAN (R 4.2.0)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.2.0)
## mime 0.12 2021-09-28 [2] CRAN (R 4.2.0)
## miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.2.0)
## munsell 0.5.0 2018-06-12 [2] CRAN (R 4.2.0)
## nlme 3.1-162 2023-01-31 [1] CRAN (R 4.2.0)
## nnet 7.3-19 2023-05-03 [1] CRAN (R 4.2.0)
## openxlsx * 4.2.5.2 2023-02-06 [1] CRAN (R 4.2.0)
## parallelly 1.35.0 2023-03-23 [1] CRAN (R 4.2.0)
## patchwork 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
## pbapply 1.7-0 2023-01-13 [1] CRAN (R 4.2.0)
## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0)
## pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.2.0)
## pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
## plotly 4.10.1 2022-11-07 [1] CRAN (R 4.2.0)
## plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.0)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0)
## polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.2.0)
## preprocessCore 1.60.2 2023-01-19 [1] Bioconductor
## prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.2.0)
## processx 3.8.1 2023-04-18 [1] CRAN (R 4.2.0)
## profvis 0.3.8 2023-05-02 [1] CRAN (R 4.2.0)
## progressr 0.13.0 2023-01-10 [1] CRAN (R 4.2.0)
## promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.2.0)
## ps 1.7.5 2023-04-18 [1] CRAN (R 4.2.0)
## purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.0)
## RANN 2.6.1 2019-01-08 [2] CRAN (R 4.2.0)
## RColorBrewer 1.1-3 2022-04-03 [2] CRAN (R 4.2.0)
## Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
## RcppAnnoy 0.0.20 2022-10-27 [1] CRAN (R 4.2.0)
## RcppRoll 0.3.0 2018-06-05 [2] CRAN (R 4.2.0)
## RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.2.0)
## remotes 2.4.2 2021-11-30 [2] CRAN (R 4.2.0)
## reshape2 1.4.4 2020-04-09 [2] CRAN (R 4.2.0)
## reticulate 1.28 2023-01-27 [1] CRAN (R 4.2.0)
## rlang 1.1.1 2023-04-28 [1] CRAN (R 4.2.0)
## rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.2.0)
## ROCR 1.0-11 2020-05-02 [2] CRAN (R 4.2.0)
## rpart 4.1.19 2022-10-21 [1] CRAN (R 4.2.0)
## Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
## RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.2.0)
## rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
## Rtsne 0.16 2022-04-17 [2] CRAN (R 4.2.0)
## S4Vectors 0.36.2 2023-02-26 [1] Bioconductor
## sass 0.4.5 2023-01-24 [1] CRAN (R 4.2.0)
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
## scattermore 0.8 2022-02-14 [1] CRAN (R 4.2.0)
## sctransform 0.3.5 2022-09-21 [1] CRAN (R 4.2.0)
## sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.2.0)
## Seurat * 4.3.0 2022-11-18 [1] CRAN (R 4.2.0)
## SeuratObject * 4.1.3 2022-11-07 [1] CRAN (R 4.2.0)
## shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.0)
## Signac * 1.9.0 2022-12-08 [1] CRAN (R 4.2.0)
## sp 1.6-0 2023-01-19 [1] CRAN (R 4.2.0)
## spatstat.data 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.explore 3.1-0 2023-03-14 [1] CRAN (R 4.2.0)
## spatstat.geom 3.1-0 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.random 3.1-4 2023-03-13 [1] CRAN (R 4.2.0)
## spatstat.sparse 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.utils 3.0-2 2023-03-11 [1] CRAN (R 4.2.0)
## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
## stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
## survival 3.5-5 2023-03-12 [1] CRAN (R 4.2.0)
## tensor 1.5 2012-05-05 [2] CRAN (R 4.2.0)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
## tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.2.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
## uwot 0.1.14 2022-08-22 [1] CRAN (R 4.2.0)
## vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.2.0)
## viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.2.0)
## WGCNA * 1.72-1 2023-01-18 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [2] CRAN (R 4.2.0)
## xfun 0.39 2023-04-20 [1] CRAN (R 4.2.0)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.2.0)
## XVector 0.38.0 2022-11-01 [1] Bioconductor
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
## zip 2.3.0 2023-04-17 [1] CRAN (R 4.2.0)
## zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
## zoo 1.8-12 2023-04-13 [1] CRAN (R 4.2.0)
##
## [1] /gpfs/gibbs/project/ya-chi_ho/jac369/R/4.2
## [2] /vast/palmer/apps/avx2/software/R/4.2.0-foss-2020b/lib64/R/library
##
## ------------------------------------------------------------------------------